Novel nucleotide and amino acid sequences, and assays and methods of use thereof for diagnosis

ABSTRACT

Novel splice variants, amino acid sequences and nucleotide sequences thereof, and methods of using same.

FIELD OF THE INVENTION

The present invention is related to novel nucleotide and proteinsequences, and assays and methods of use thereof.

BACKGROUND OF THE INVENTION

Diagnostic markers are important for early diagnosis of many diseases,as well as predicting response to treatment, monitoring treatment anddetermining prognosis of such diseases.

Serum markers are examples of such diagnostic markers and are used fordiagnosis of many different diseases. Such serum markers typicallyencompass secreted proteins and/or peptides; however, some serum markersmay be released to the blood upon tissue lysis, such as from myocardialinfarction (for example Troponin-I). Serum markers can also be used asrisk factors for disease (for example base-line levels of CRP, as apredictor of cardiovascular disease), to monitor disease activity andprogression (for example, determination of CRP levels to monitor acutephase inflammatory response) and to predict and monitor drug response(for example, as shedded fragments of the protein Erb-B2).

Immunohistochemistry (IHC) is the study of distribution of an antigen ofchoice in a sample based on specific antibody-antigen binding, typicallyon tissue slices. The antibody features a label which can be detected,for example as a stain which is detectable under a microscope. Thetissue slices are prepared by being fixed. IHC is therefore particularlysuitable for antibody-antigen reactions that are not disturbed ordestroyed by the process of tissue fixation.

IHC permits determining the localization of binding, and hence mappingof the presence of the antigen within the tissue and even withindifferent compartments in the cell. Such mapping can provide usefuldiagnostic information, including:

1) the histological type of the tissue sample2) the presence of specific cell types within the sample3) information on the physiological and/or pathological state of cells(e.g. which phase of the cell-cycle they are in)4) the presence of disease related changes within the sample5) differentiation between different specific disease subtypes where itis already known the tissue is of disease state (for example, thedifferentiation between different tumor types when it is already knownthe sample was taken from cancerous tissue).

IHC information is valuable for more than diagnosis. It can also be usedto determine prognosis and therapy treatment (as in the case of HER-2 inbreast cancer) and monitor disease.

IHC protein markers could be from any cellular location. Most oftenthese markers are membrane proteins but secreted proteins orintracellular proteins (including intranuclear) can be used as an IHCmarker too.

IHC has at least two major disadvantages. It is performed on tissuesamples and therefore a tissue sample has to be collected from thepatient, which most often requires invasive procedures like biopsyassociated with pain, discomfort, hospitalization and risk of infection.In addition, the interpretation of the result is observer dependant andtherefore subjective. There is no measured value but rather only anestimation (on a scale of 1-4) of how prevalent the antigen on targetis.

SUMMARY OF THE INVENTION

The present invention provides, in different embodiments, many novelamino acid and nucleic acid sequences, which may optionally be used asdiagnostic markers.

In some embodiments, the present invention provides a number ofdifferent variants of known proteins, which are expressed in serum andmay optionally be used as diagnostic markers, which in some embodiments,are serum markers, or in other embodiments, are IHC markers. The presentinvention therefore overcomes the many deficiencies of the backgroundart with regard to the need to obtain tissue samples and subjectiveinterpretations of results. In one embodiment, tissue specific markersare identifible in serum or plasma. In some embodiments, a simple bloodtest can provide qualitative and/or quantitative indicators forexpression of a desired marker, for example, serving as an indicator forvarious diseases and/or pathological conditions. The markers presentedin the present invention can also potentially be used for in-vivoimaging applications.

The present invention also provides, in some embodiments, a number ofdifferent variants, which serve as IHC markers or indicators, which insome embodiments, serve as diagnostic markers, for example as serummarkers, or IHC markers. [The present invention therefore overcomes themany deficiencies of the background art with regard to the need toobtain tissue samples and subjective interpretations of results. Forexample, serum markers require only a simple blood test and their resultis typically a scientifically measured number. As IHC markers, thevariants of the present invention may also provide different and/orbetter measurement parameters for various diseases and/or pathologicalconditions.

Other variants are also provided by the present invention as describedin greater detail below.

The diseases for which such variants may be useful as diagnostic markersare described in greater detail below. The variants themselves aredescribed by “cluster” or by gene, as these variants are splice variantsof known proteins. In some embodiments, the term “marker-detectabledisease” refers to a disease that may be detected by a particularmarker, with regard to the description of such diseases below. In someembodiments, the markers of the present invention, alone or incombination, show a high degree of differential detection betweendisease and non-disease states.

The present invention relates, in some embodiments, to diagnostic assaysfor disease detection, which in some embodiments, utilizes a biologicalsample taken from a subject (patient), which for example may comprise abody fluid or secretion including but not limited to seminal plasma,blood, serum, urine, prostatic fluid, seminal fluid, semen, the externalsecretions of the skin, respiratory, intestinal, and genitourinarytracts, tears, cerebrospinal fluid, sputum, saliva, milk, peritonealfluid, pleural fluid, cyst fluid, secretions of the breast ductal system(and/or lavage thereof), broncho alveolar lavage, lavage of thereproductive system, lavage of any other part of the body or system inthe body, stool or a tissue sample, or any combination thereof. In someembodiments, the term encompasses samples of in vivo cell cultureconstituents. The sample can optionally be diluted with a suitableeluant before contacting the sample to an antibody and/or performing anyother diagnostic assay.

In some embodiments of the present invention, nucleic acids, orpolypeptides, having a sequence as described herein, or homologuesthereof.

In some embodiments, the terms “homology”, “homologue” or “homologous”,in any instance, indicate that the sequence referred to, whether anamino acid sequence, or a nucleic acid sequence, exhibits, in oneembodiment at least 70% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 72% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 75% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 77% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 80% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 82% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 85% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 87% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 90% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 92% correspondence with the indicated sequence. Inanother embodiment, the amino acid sequence or nucleic acid sequenceexhibits at least 95% or more correspondence with the indicatedsequence. In another embodiment, the amino acid sequence or nucleic acidsequence exhibits 95%-100% correspondence to the indicated sequence.Similarly, in some embodiments, the reference to a correspondence to aparticular sequence includes both direct correspondence, as well ashomology to that sequence as herein defined.

In some embodiments, this invention provides an isolated polynucleotidecomprising a nucleic acid having a sequence corresponding to, orhomologous to that set forth in SEQ ID NOs: 1-15, 61-64, 96-98, 114-126,189-195, 211-214, 235, 244, 152-253, 305-306, 340-344.

In some embodiments, this invention provides an isolated polynucleotidecomprising a nucleic acid having a sequence corresponding to, orhomologous to that set forth in SEQ ID NOs: 32-60, 71-95, 103-113,139-188, 196-219, 220-234, 237-243, 246-251, 256-304, 309-339, 350-358,502-530.

In some embodiments, this invention provides an isolated protein orpolypeptide having an amino acid sequence corresponding to, orhomologous to that set forth in SEQ ID NOs:16-31, 65-70, 99-102,127-138, 215-219, 236, 245, 254-255, 307-308.

In some embodiments, the proteins or polypeptides of this inventioncomprise chimeric protein or polypeptides.

In some embodiments, the terms “chimeric protein or polypeptide”, or“chimera” refers to an assembly or a string of amino acids in aparticular sequence, or nucleotides encoding the same, respectively,which does not correspond to the sequence of the known (wild type)polypeptide or protein, or nucleic acid, respectively. In someembodiments, the variants of this invention are derived by the by theassembly or stringing of amino acids or polynucleotides encoding thesame, from two exons, or an exon and an intron, or fragments thereof, orsegments having sequences with the indicated homology.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that set forth in SEQ ID NO:16 (HSFLT_P6).

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatset forth in HSFLT_P6 (SEQ ID NO:16), comprising a first amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least95%, homologous to a polypeptide having the sequence MTAP (SEQ ID NO:459) corresponding to amino acids 1-4 of HSFLT_P6 (SEQ ID NO:16), and asecond amino acid sequence being at least 90% homologous to amino acids172-1338 of VGR1_HUMAN_V1 (SEQ ID NO: 575), which also corresponds toamino acids 5-1171 of HSFLT_P6 (SEQ ID NO:16), wherein said first aminoacid sequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptidecomprising a head portion of an HSFLT_P6 (SEQ ID NO:16), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequence MTAP (SEQID NO: 459) of HSFLT_P6 (SEQ ID NO:16).

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatas set forth in HSFLT_P6 (SEQ ID NO:16), comprising a first amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least95%, homologous to a polypeptide having the sequence MTAP (SEQ ID NO:459) corresponding to amino acids 1-4 of HSFLT_P6 (SEQ ID NO:16), asecond amino acid sequence being at least 90% homologous to amino acids172-656 of P17948-2 (SEQ ID NO:360), which also corresponds to aminoacids 5-489 of HSFLT_P6 (SEQ ID NO:16), and a third amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTMGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) corresponding to amino acids 490-1171 ofHSFLT_P6 (SEQ ID NO:16), wherein said first amino acid sequence, secondamino acid sequence and third amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HSFLT_P6 (SEQ ID NO:16), comprising a polypeptidebeing at least 70%, optionally at least about 80%, preferably at leastabout 85%, more preferably at least about 90% and most preferably atleast about 95% homologous to the sequence MTAP (SEQ ID NO: 459) ofHSFLT_P6 (SEQ ID NO:16).

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P6 (SEQ ID NO:16), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTILDCHANGVPEPQITWFKNKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) of HSFLT_P6 (SEQ ID NO:16).

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatset forth in HSFLT_P7 (SEQ ID NO:17).

In some embodiments, this invention provides an isolated chimericpolypeptide as set forth in HSFLT_P7 (SEQ ID NO:17), comprising a firstamino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMPLPFQ (SEQ ID NO: 576) corresponding to amino acids 1-6 of HSFLT_P7(SEQ ID NO:17), and a second amino acid sequence being at least 90%homologous to amino acids 172-1338 of VGR1_HUMAN_V1 (SEQ ID NO: 575),which also corresponds to amino acids 7-1173 of HSFLT_P7 (SEQ ID NO:17),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HSFLT_P7 (SEQ ID NO:17), comprising a polypeptidebeing at least 70%, optionally at least about 80%, preferably at leastabout 85%, more preferably at least about 90% and most preferably atleast about 95% homologous to the sequence MPLPFQ (SEQ ID NO: 576) ofHSFLT_P7 (SEQ ID NO:17).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that, as set forth in HSFLT_P7 (SEQ ID NO:17), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMPLPFQ (SEQ ID NO: 576) corresponding to amino acids 1-6 of HSFLT_P7(SEQ ID NO:17), and a second amino acid sequence being at least 90%homologous to amino acids 172-1338 of NP_(—)002010_V1 (SEQ ID NO: 574),which also corresponds to amino acids 7-1173 of HSFLT_P7 (SEQ ID NO:17),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HSFLT_P7 (SEQ ID NO:17), comprising a polypeptidebeing at least 70%, optionally at least about 80%, preferably at leastabout 85%, more preferably at least about 90% and most preferably atleast about 95% homologous to the sequence MPLPFQ (SEQ ID NO: 576) ofHSFLT_P7 (SEQ ID NO:17).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P7 (SEQ ID NO:17), comprising afirst amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMPLPFQ (SEQ ID NO: 576) corresponding to amino acids 1-6 of HSFLT_P7(SEQ ID NO:17), a second amino acid sequence being at least 90%homologous to amino acids 172-656 of P 7948-2 (SEQ ID NO:360), whichalso corresponds to amino acids 7-491 of HSFLT_P7 (SEQ ID NO:17), and athird amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTUIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKKEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCMIRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) corresponding to amino acids 492-1173 ofHSFLT_P7 (SEQ ID NO:17), wherein said first amino acid sequence, secondamino acid sequence and third amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HSFLT_P7 (SEQ ID NO:17), comprising a polypeptidebeing at least 70%, optionally at least about 80%, preferably at leastabout 85%, more preferably at least about 90% and most preferably atleast about 95% homologous to the sequence MPLPFQ (SEQ ID NO: 576) ofHSFLT_P7 (SEQ ID NO:17).

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P7 (SEQ ID NO:17), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTMIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) of HSFLT_P7 (SEQ ID NO:17).

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatset forth in HSFLT_P10 (SEQ ID NO:18).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P10 (SEQ ID NO:18), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-705 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-705 of HSFLT_P10 (SEQ ID NO:18), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO: 462) corresponding to aminoacids 706-733 of HSFLT_P10 (SEQ ID NO:18), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P10 (SEQ ID NO:18), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO: 462) of HSFLT_P10 (SEQ IDNO:18).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P10 (SEQ ID NO:18), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-656 of P17948-2 (SEQ ID NO:360), which also corresponds to amino acids1-656 of HSFLT_P10 (SEQ ID NO:18), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPELYTSTSPSSSSSSPLSSSSSSSSSSSS(SEQ ID NO: 463) corresponding to amino acids 657-733 of HSFLT_P10 (SEQID NO:18), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P10 (SEQ ID NO:18), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPELYTSTSPSSSSSSPLSSSSSSSSSSSS(SEQ ID NO: 463) of HSFLT_P10 (SEQ ID NO:18).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P10 (SEQ ID NO:18), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-705 of NP_(—)002010 (SEQ ID NO: 531), which also corresponds to aminoacids 1-705 of HSFLT_P10 (SEQ ID NO:18), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO: 462) corresponding to aminoacids 706-733 of HSFLT_P10 (SEQ ID NO:18), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatset forth in HSFLT_P11 (SEQ ID NO:19).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P11 (SEQ ID NO:19), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-706 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-706 of HSFLT_P11 (SEQ ID NO:19), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence SANTAVNKKTEI (SEQ ID NO:464) corresponding to amino acids 707-718 of HSFLT_P11 (SEQ ID NO:19),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P11 (SEQ ID NO:19), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceSANTAVNKKTEI (SEQ ID NO: 464) of HSFLT_P11 (SEQ ID NO:19).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P11 (SEQ ID NO:19), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-656 of P17948-2 (SEQ ID NO:360), which also corresponds to amino acids1-656 of HSFLT_P111 (SEQ ID NO:19), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGSANTAVNKKTEI (SEQ IDNO: 465) corresponding to amino acids 657-718 of HSFLT_P11 (SEQ IDNO:19), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P11 (SEQ ID NO:19), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGSANTAVNKKTEI (SEQ IDNO: 465) of HSFLT_P11 (SEQ ID NO:19).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P11 (SEQ ID NO:19), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-706 of NP_(—)002010 (SEQ ID NO: 531), which also corresponds to aminoacids 1-706 of HSFLT_P11 (SEQ ID NO:19), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence SANTAVNKKTEI (SEQ ID NO:464) corresponding to amino acids 707-718 of HSFLT_P11 (SEQ ID NO:19),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, such isolated chimeric proteins or polypeptides maycomprise an amino acid sequence corresponding to or homologous to thatset forth in HSFLT_P13 (SEQ ID NO:20).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P13 (SEQ ID NO:20), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-706 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-706 of HSFLT_P13 (SEQ ID NO:20), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceKRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO: 466) corresponding to aminoacids 707-736 of HSFLT_P13 (SEQ ID NO:20), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P13 (SEQ ID NO:20), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceKRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO: 466) of HSFLT_P13 (SEQ IDNO:20).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P13 (SEQ ID NO:20), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-656 of P17948-2 (SEQ ID NO:360), which also corresponds to amino acids1-656 of HSFLT_P13 (SEQ ID NO:20), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGKRLFFLPFIISHLSSAPLSLNSPVTCFQYV(SEQ ID NO: 467) corresponding to amino acids 657-736 of HSFLT_P13 (SEQID NO:20), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P13 (SEQ ID NO:20), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGKRLFFLPFIISHLSSAPLSLNSPVTCFQYV(SEQ ID NO: 467) of HSFLT_P13 (SEQ ID NO:20).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P13 (SEQ ID NO:20), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-706 of NP_(—)002010 (SEQ ID NO: 531), which also corresponds to aminoacids 1-706 of HSFLT_P13 (SEQ ID NO:20), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceKRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO: 466) corresponding to aminoacids 707-736 of HSFLT_P13 (SEQ ID NO:20), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P14 (SEQ ID NO:21), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-517 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-517 of HSFLT_P14 (SEQ ID NO:21), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceYLDIRTEEQIFSFIQKTQTLKLTVSCKAAF (SEQ ID NO: 468) corresponding to aminoacids 518-547 of HSFLT_P14 (SEQ ID NO:21), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P14 (SEQ ID NO:21), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceYLDIRTEEQIFSFIQKTQTLKLTVSCKAAF (SEQ ID NO: 468) of HSFLT_P14 (SEQ IDNO:21).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P15 (SEQ ID NO:22), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-329 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-329 of HSFLT_P15 (SEQ ID NO:22), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGKHSSALPTHAMLSNHCRCLCSLNKSVFCWPRVTLS (SEQ ID NO: 469) corresponding toamino acids 330-365 of HSFLT_P15 (SEQ ID NO:22), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P15 (SEQ ID NO:22), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceGKHSSALPTHAMLSNTICRCLCSLNKSVFCWPRVTLS (SEQ ID NO: 469) of HSFLT_P15 (SEQID NO:22).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P16 (SEQ ID NO:23), comprisingan amino acid sequence being at least 90% homologous to amino acids906-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-433 of HSFLT_P16 (SEQ ID NO:23).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P16 (SEQ ID NO:23), comprisingan amino acid sequence being at least 90% homologous to amino acids906-1338 of NP_(—)002010 (SEQ ID NO: 531), which also corresponds toamino acids 1-433 of HSFLT_P16 (SEQ ID NO:23).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P17 (SEQ ID NO:24), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-171 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-171 of HSFLT_P17 (SEQ ID NO:24), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceVNLNTAILSILSLQISIMKFYSFYLSGIISLQTPGLLSGLSCN (SEQ ID NO: 470)corresponding to amino acids 172-214 of HSFLT_P17 (SEQ ID NO:24),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P17 (SEQ ID NO:24), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceVNLNTAILSILSLQISIMKFYSFYLSGIISLQTPGLLSGLSCN (SEQ ID NO: 470) ofHSFLT_P17 (SEQ ID NO:24).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P18 (SEQ ID NO:25), comprisingan amino acid sequence being at least 90% homologous to amino acids996-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-343 of HSFLT_P18 (SEQ ID NO:25).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P18 (SEQ ID NO:25), comprisingan amino acid sequence being at least 90% homologous to amino acids996-1338 of NP_(—)002010 (SEQ ID NO: 531), which also corresponds toamino acids 1-343 of HSFLT_P18 (SEQ ID NO:25).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P19 (SEQ ID NO:26), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-129 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-129 of HSFLT_P19 (SEQ ID NO:26), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGKTSIFYILFAFALQMSHKSTLIHKGCFPSEYERNGLGKRFHPSCRHFRGCQF (SEQ ID NO: 471)corresponding to amino acids 130-183 of HSFLT_P19 (SEQ ID NO:26),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides isolated polypeptideencoding for an edge portion of HSFLT_P19 (SEQ ID NO:26), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceGKTSIFYILFAFALQMSHKSTLIHWKGCFPSEYERNGLGKRFHPSCRHFRGCQF (SEQ ID NO: 471)of HSFLT_P19 (SEQ ID NO:26).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P20 (SEQ ID NO:27), comprisingan amino acid sequence being at least 90% homologous to amino acids1133-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds toamino acids 1-206 of HSFLT_P20 (SEQ ID NO:27).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P21 (SEQ ID NO:28), comprisingan amino acid sequence being at least 90% homologous to amino acids1220-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds toamino acids 1-119 of HSFLT_P21 (SEQ ID NO:28).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P41 (SEQ ID NO:29), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceLWAACPAQACSGNAGQERGGLQSAAGLPSQPSCFLQTGVGLANQ (SEQ ID NO: 577)corresponding to amino acids 1-44 of HSFLT_P41 (SEQ ID NO:29), and asecond amino acid sequence being at least 90% homologous to amino acids903-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 45-480 of HSFLT_P41 (SEQ ID NO:29), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides isolated polypeptideencoding for a head of HSFLT_P41 (SEQ ID NO:29), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceLWAACPAQACSGNAGQERGGLQSAAGLPSQPSCFLQTGVGLANQ (SEQ ID NO: 577) ofHSFLT_P41 (SEQ ID NO:29).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P48 (SEQ ID NO:30), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-517 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-517 of HSFLT_P48 (SEQ ID NO:30), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence LPPANSSFMLPPTSFSSNYFHFLP(SEQ ID NO: 472) corresponding to amino acids 518-541 of HSFLT_P48 (SEQID NO:30), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides isolated polypeptideencoding for an edge portion of HSFLT_P48 (SEQ ID NO:30), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceLPPANSSFMLPPTSFSSNYFHFLP (SEQ ID NO: 472) of HSFLT_P48 (SEQ ID NO:30).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSFLT_P49 (SEQ ID NO:31), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-553 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds to aminoacids 1-553 of HSFLT_P49 (SEQ ID NO:31), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence ELSNFECLHPCSQE (SEQ IDNO: 473) corresponding to amino acids 554-567 of HSFLT_P49 (SEQ IDNO:31), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSFLT_P49 (SEQ ID NO:31), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceELSNFECLHPCSQE (SEQ ID NO: 473) of HSFLT_P49 (SEQ ID NO:31).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P5 (SEQ ID NO:65), comprisinga first amino acid sequence being at least 90% homologous to amino acids35-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds to aminoacids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 35-64 of HSI1RA_P5 (SEQ IDNO:65), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSI1RA_P5 (SEQ ID NO:65), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) of HSI1RA_P5 (SEQ IDNO:65).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P5 (SEQ ID NO:65), comprisinga first amino acid sequence being at least 90% homologous to amino acids17-50 of NP_(—)000568 (SEQ ID NO: 532), which also corresponds to aminoacids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 35-64 of HSI1RA_P5 (SEQ IDNO:65), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P5 (SEQ ID NO:65), comprisinga first amino acid sequence being at least 90% homologous to amino acids35-68 of NP_(—)776214 (SEQ ID NO: 534), which also corresponds to aminoacids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 35-64 of HSI1RA_P5 (SEQ IDNO:65), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P5 (SEQ ID NO:65), comprisinga first amino acid sequence being at least 90% homologous to amino acids38-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds to aminoacids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 35-64 of HSI1RA_P5 (SEQ IDNO:65), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P6 (SEQ ID NO:66), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds to aminoacids 1-68 of HSI1RA_P6 (SEQ ID NO:66), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 69-98 of HSI1RA_P6 (SEQ IDNO:66), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P6 (SEQ ID NO:66), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) corresponding to amino acids 1-21of HSI1RA_P6 (SEQ ID NO:66), a second amino acid sequence being at least90% homologous to amino acids 4-50 of P18510-2 (SEQ ID NO:373), whichalso corresponds to amino acids 22-68 of HSI1RA_P6 (SEQ ID NO:66), and athird amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 69-98 of HSI1RA_P6 (SEQ ID NO:66), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

An isolated polypeptide encoding for a head of HSI1RA_P6 (SEQ ID NO:66),comprising a polypeptide being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) of HSI1RA_P6 (SEQ ID NO:66).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P6 (SEQ ID NO:66), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) corresponding toamino acids 1-34 of HSI1RA_P6 (SEQ ID NO:66), a second amino acidsequence being at least 90% homologous to amino acids 1-34 of P18510-4(SEQ ID NO:375), which also corresponds to amino acids 35-68 ofHSI1RA_P6 (SEQ ID NO:66), and a third amino acid sequence being at least70%, optionally at least 80%, preferably at least 85%, more preferablyat least 90% and most preferably at least 95% homologous to apolypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ IDNO: 474) corresponding to amino acids 69-98 of HSI1RA_P6 (SEQ ID NO:66),wherein said first amino acid sequence, second amino acid sequence andthird amino acid sequence are contiguous and in a sequential order.

An isolated polypeptide encoding for a head of HSI1RA_P6 (SEQ ID NO:66),comprising a polypeptide being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) of HSI1RA_P6 (SEQ IDNO:66).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P13 (SEQ ID NO:67), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceMAL (SEQ ID NO: 580) corresponding to amino acids 1-3 of HSI1RA_P13 (SEQID NO:67), a second amino acid sequence being at least 90% homologous toamino acids 22-68 of IL1X_HUMAN (SEQ ID NO: 372), which also correspondsto amino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67), and a third amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P13 (SEQ ID NO:67), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-50 of NP_(—)000568 (SEQ ID NO: 532), which also corresponds to aminoacids 1-50 of HSI1RA_P13 (SEQ ID NO:67), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P13 (SEQ ID NO:67), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-3 of P18510-3 (SEQ ID NO:374), which also corresponds to amino acids1-3 of HSI1RA_P13 (SEQ ID NO:67), a second amino acid sequence being atleast 90% homologous to amino acids 25-71 of P18510-3 (SEQ ID NO:374),which also corresponds to amino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67),and a third amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HSI1RA_P13 (SEQ ID NO:67),comprising a polypeptide having a length “n”, wherein n is at leastabout 10 amino acids in length, optionally at least about 20 amino acidsin length, preferably at least about 30 amino acids in length, morepreferably at least about 40 amino acids in length and most preferablyat least about 50 amino acids in length, wherein at least two aminoacids comprise LE, having a structure as follows: a sequence startingfrom any of amino acid numbers 3−x to 3; and ending at any of amino acidnumbers 4+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P13 (SEQ ID NO:67), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceMAL (SEQ ID NO: 580) corresponding to amino acids 1-3 of HSI1RA_P13 (SEQID NO:67), a second amino acid sequence being at least 90% homologous toETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 22-68 of NP_(—)776214 (SEQ ID NO: 534), which also corresponds toamino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67), and a third amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P13 (SEQ ID NO:67), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMALETICRPSGRKSSK (SEQ ID NO: 581) corresponding to amino acids 1-16 ofHSI1RA_P13 (SEQ ID NO:67), a second amino acid sequence being at least90% homologous to amino acids 1-34 of P18510-4 (SEQ ID NO:375), whichalso corresponds to amino acids 17-50 of HSI1RA_P13 (SEQ ID NO:67), anda third amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

An isolated polypeptide encoding for a head of HSI1RA_P13 (SEQ IDNO:67), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMALETICRPSGRKSSK (SEQ ID NO: 581) of HSI1RA_P13 (SEQ ID NO:67).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P14 (SEQ ID NO:68), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-24 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds to aminoacids 1-24 of HSI1RA_P14 (SEQ ID NO:68), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence GGL (SEQ ID NO: 477)corresponding to amino acids 25-27 of HSI1RA_P14 (SEQ ID NO:68), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSI1RA_P14 (SEQ ID NO:68), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequence GGL (SEQID NO: 477) of HSI1RA_P14 (SEQ ID NO:68).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds to aminoacids 1-68 of HSI1RA_P16 (SEQ ID NO:69), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSI1RA_P16 (SEQ ID NO:69), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequence DRCGTH(SEQ ID NO: 478) of HSI1RA_P16 (SEQ ID NO:69).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) corresponding to amino acids 1-21of HSI1RA_P16 (SEQ ID NO:69), a second amino acid sequence being atleast 90% homologous to amino acids 4-50 of P18510-2 (SEQ ID NO:373),which also corresponds to amino acids 22-68 of HSI1RA_P16 (SEQ IDNO:69), and a third amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence DRCGTH (SEQ ID NO: 478) corresponding to amino acids 69-74 ofHSI1RA_P16 (SEQ ID NO:69), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

An isolated polypeptide encoding for a head of HSI1RA_P16 (SEQ IDNO:69), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) of HSI1RA_P16 (SEQ ID NO:69).

An isolated chimeric polypeptide as set forth in HSI1RA_P16 (SEQ IDNO:69), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) correspondingto amino acids 1-21 of HSI1RA_P16 (SEQ ID NO:69), a second amino acidsequence being at least 90% homologous to amino acids 25-71 ofNP_(—)776213 (SEQ ID NO: 533), which also corresponds to amino acids22-68 of HSI1RA_P16 (SEQ ID NO:69), and a third amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), whereinsaid first amino acid sequence, second amino acid sequence and thirdamino acid sequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) corresponding toamino acids 1-34 of HSI1RA_P16 (SEQ ID NO:69), a second amino acidsequence being at least 90% homologous to amino acids 1-34 of P18510-4(SEQ ID NO:375), which also corresponds to amino acids 35-68 ofHSI1RA_P16 (SEQ ID NO:69), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence DRCGTH (SEQ ID NO: 478) corresponding toamino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), wherein said first aminoacid sequence, second amino acid sequence and third amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HSI1RA_P16 (SEQ ID NO:69), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) of HSI1RA_P16 (SEQID NO:69).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds to aminoacids 1-68 of HSI1RA_P16 (SEQ ID NO:69), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) corresponding to amino acids 1-21of HSI1RA_P16 (SEQ ID NO:69), a second amino acid sequence being atleast 90% homologous to amino acids 4-50 of P18510-2 (SEQ ID NO:373),which also corresponds to amino acids 22-68 of HSI1RA_P16 (SEQ IDNO:69), and a third amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence DRCGTH (SEQ ID NO: 478) corresponding to amino acids 69-74 ofHSI1RA_P16 (SEQ ID NO:69), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) corresponding to amino acids 1-21of HSI1RA_P16 (SEQ ID NO:69), a second amino acid sequence being atleast 90% homologous amino acids 25-71 of NP_(—)776213 (SEQ ID NO: 533),which also corresponds to amino acids 22-68 of HSI1RA_P16 (SEQ IDNO:69), and a third amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence DRCGTH (SEQ ID NO: 478) corresponding to amino acids 69-74 ofHSI1RA_P16 (SEQ ID NO:69), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P16 (SEQ ID NO:69), comprisinga first amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95%, homologous to a polypeptide having the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) corresponding toamino acids 1-34 of HSI1RA_P16 (SEQ ID NO:69), a second amino acidsequence being at least 90% homologous to amino acids 1-34 of P18510-4(SEQ ID NO:375), which also corresponds to amino acids 35-68 ofHSI1RA_P16 (SEQ ID NO:69), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence DRCGTH (SEQ ID NO: 478) corresponding toamino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), wherein said first aminoacid sequence, second amino acid sequence and third amino acid sequenceare contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P17 (SEQ ID NO:70), comprisinga first amino acid sequence being at least 90% homologous to amino acids35-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds to aminoacids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid, first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P17 (SEQ ID NO:70), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-34 of P18510-4 (SEQ ID NO:375), which also corresponds to amino acids1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P17 (SEQ ID NO:70), comprisinga first amino acid sequence being at least 90% homologous to amino acids17-50 of NP_(—)000568 (SEQ ID NO: 532), which also corresponds to aminoacids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P17 (SEQ ID NO:70), comprisinga first amino acid sequence being at least 90% homologous to amino acids35-68 of NP_(—)776214 (SEQ ID NO: 534), which also corresponds to aminoacids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSI1RA_P17 (SEQ ID NO:70), comprisinga first amino acid sequence being at least 90% homologous to amino acids38-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds to aminoacids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSPLGF_(—)1_P4 (SEQ ID NO:99),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-140 of P49763-2 (SEQ ID NO: 536), which also correspondsto amino acids 1-140 of HSPLGF_(—)1_P4 (SEQ ID NO:99), and a secondamino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceSHLVLTLGLLQEETQGQGEEEEREAETHRLPPVRRCCSPEVTHPLEERDPAPGSCIYYRHTLQ (SEQ IDNO: 480) corresponding to amino acids 141-203 of HSPLGF_(—)1_P4 (SEQ IDNO:99), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HSPLGF_(—)1_P4 (SEQ ID NO:99),comprising an amino acid sequence being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence SHLVLTLGLLQEETQGQGEEEEREAETHRLPPVRRCCSPEVTBPLEERDPAPGSCIYYRHTLQ(SEQ ID NO: 480) of HSPLGF_(—)1_P4 (SEQ ID NO:99).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HSPLGF_(—)1_P13 (SEQ ID NO:101),comprising a amino acid sequence being at least 90% homologous to aminoacids 1-141 of P49763-2 (SEQ ID NO: 536), which also corresponds toamino acids 1-141 of HSPLGF_(—)1_P13 (SEQ ID NO:101).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P3 (SEQ ID NO:127),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MHQAGYPGCRGA (SEQ ID NO: 582) corresponding to amino acids 1-12of HUMSP18A_P3 (SEQ ID NO:127), a second amino acid sequence being atleast 90% homologous to amino acids 1-285 of PSPB_HUMAN (SEQ ID NO:406),which also corresponds to amino acids 13-297 of HUMSP18A_P3 (SEQ IDNO:127), and a third amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence SEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) corresponding to aminoacids 298-319 of HUMSP18A_P3 (SEQ ID NO:127), wherein said first aminoacid sequence, second amino acid sequence and third amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMSP18A_P3 (SEQ ID NO:127), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMHQAGYPGCRGA (SEQ ID NO: 582) of HUMSP18A_P3 (SEQ ID NO:127).

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P3 (SEQ ID NO:127), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceSEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) of HUMSP18A_P3 (SEQ ID NO:127).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P20 (SEQ ID NO:128),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO:583) corresponding to amino acids 1-49 of HUMSP18A_P20 (SEQ ID NO:128),and a second amino acid sequence being at least 90% homologous to aminoacids 66-381 of PSPB_HUMAN (SEQ ID NO:406), which also corresponds toamino acids 50-365 of HUMSP18A_P20 (SEQ ID NO:128), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMSP18A_P20 (SEQ ID NO:128), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO: 583) ofHUMSP18A_P20 (SEQ ID NO:128).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P22 (SEQ ID NO:129),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO:583) corresponding to amino acids 1-49 of HUMSP18A_P22 (SEQ ID NO:129),a second amino acid sequence being at least 90% homologous to aminoacids 66-131 of PSPB_HUMAN (SEQ ID NO:406), which also corresponds toamino acids 50-115 of HUMSP18A_P22 (SEQ ID NO:129), and a third aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHKHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHTHTQHPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTQHTHSTPAGHTHTHTHPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLHMLTHLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) corresponding to amino acids 116-344 ofHUMSP18A_P22 (SEQ ID NO:129), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P22 (SEQ ID NO:129), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHKHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHTHTQHPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHTHSTPAGHTHTHTHPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLTHMLTHLFILTYMLMLIHITQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) of HUMSP18A_P22 (SEQ ID NO:129).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P38 (SEQ ID NO:130),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-285 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-285 of HUMSP18A_P38 (SEQ ID NO:130), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence SEPTAPSLAQCLLSSSPYPATA(SEQ ID NO:481) corresponding to amino acids 286-307 of HUMSP18A_P38(SEQ ID NO:130), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P38 (SEQ ID NO:130), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceSEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) of HUMSP18A_P38 (SEQ ID NO:130).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P39 (SEQ ID NO:131),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-334 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-334 of HUMSP18A_P39 (SEQ ID NO:131), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence LAPVC (SEQ ID NO: 484)corresponding to amino acids 335-339 of HUMSP18A_P39 (SEQ ID NO:131),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P39 (SEQ ID NO:131), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceLAPVC(SEQ ID NO:484) of HUMSP18A_P39 (SEQ ID NO:131).

{In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P41 (SEQ ID NO:132),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-224 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-224 of HUMSP18A_P41 (SEQ ID NO:132), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceVRHPGPHRAQEHTTCSSLQLPPLSQLTPPSGPSWLPEVRRGESRLCIAPTQGTLGLRLRPGRCQAYSSCNKH(SEQ ID NO: 485) corresponding to amino acids 225-297 of HUMSP18A_P41(SEQ ID NO:132), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P41 (SEQ ID NO:132), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceVRHPGPHRAQEHITHTCSSLQLPPLSQLTPPSGPSWLPEVRRGESRLCIAPTQGTLGLRLRPGRCQAYSSCNKH(SEQ ID NO:485) of HUMSP18A_P41 (SEQ ID NO:132).

{In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P43 (SEQ ID NO:133),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-131 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-131 of HUMSP18A_P43 (SEQ ID NO:133), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHKHTAPQPAGHTHTUTHNTPAGRTHTHTVPQLAGHTHTQHPIQTHTHQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHHTHSTPAGHTHTHTBPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTTIPYTLTLTHMLTBLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) corresponding to amino acids 132-360 ofHUMSP18A_P43 (SEQ ID NO:133), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P43 (SEQ ID NO:133), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceVRAASSPPACLPTQAPVPTHGEPHTQBPSQPDHTHFHTHTTAPKPARHKHTAPQPAGHETHTHNTPAGRTHTHTVPQLAGHTHTQBPIQTHTHTQYPSQLE-fHTHTALHPDTYPHSTPASQHTHTQHTHSTPAGH-FHTHTHPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLTHMLTBLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) of HUMSP18A_P43 (SEQ ID NO:133).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P45 (SEQ ID NO:134),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-65 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-65 of HUMSP18A_P45 (SEQ ID NO:134), a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence RTSPLELGASPTHVSSTLGPLPPQ(SEQ ID NO: 487) corresponding to amino acids 66-89 of HUMSP18A_P45 (SEQID NO:134), and a third amino acid sequence being at least 90%homologous to amino acids 66-381 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 90-405 of HUMSP18A_P45 (SEQ ID NO:134),wherein said first amino acid sequence, second amino acid sequence andthird amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P45 (SEQ ID NO:134), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO: 487) of HUMSP18A_P45 (SEQ IDNO:134).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P48 (SEQ ID NO:135),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-225 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-225 of HUMSP18A_P48 (SEQ ID NO:135), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence RRQENGCRETLSATSACP (SEQID NO: 488) corresponding to amino acids 226-243 of HUMSP18A_P48 (SEQ IDNO:135), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P48 (SEQ ID NO:135), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceRRQENGCRETLSATSACP (SEQ ID NO: 488) of HUMSP18A_P48 (SEQ ID NO:135).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P49 (SEQ ID NO:136),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-361 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-361 of HUMSP18A_P49 (SEQ ID NO:136), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence KKTPSFKVLQYGQTWWLTPAIPAP(SEQ ID NO: 489) corresponding to amino acids 362-385 of HUMSP18A_P49(SEQ ID NO:136), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMSP18A_P49 (SEQ ID NO:136), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceKKTPSFKVLQYGQTWWLTPAIPAP (SEQ ID NO: 489) of HUMSP18A_P49 (SEQ IDNO:136).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P50 (SEQ ID NO:137),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-194 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-194 of HUMSP18A_P50 (SEQ ID NO:137), and a second aminoacid sequence being at least 90% homologous to amino acids 225-381 ofPSPB_HUMAN (SEQ ID NO:406), which also corresponds to amino acids195-351 of HUMSP18A_P50 (SEQ ID NO:137), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMSP18A_P50 (SEQ IDNO:137), comprising a polypeptide having a length “n”, wherein n is atleast about 10 amino acids in length, optionally at least about 20 aminoacids in length, preferably at least about 30 amino acids in length,more preferably at least about 40 amino acids in length and mostpreferably at least about 50 amino acids in length, wherein at least twoamino acids comprise QG, having a structure as follows: a sequencestarting from any of amino acid numbers 194−x to 194; and ending at anyof amino acid numbers 195+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMSP18A_P53 (SEQ ID NO:138),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-89 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-89 of HUMSP18A_P53 (SEQ ID NO:138), and a second aminoacid sequence being at least 90% homologous to amino acids 132-381 ofPSPB_HUMAN (SEQ ID NO:406), which also corresponds to amino acids 90-339of HUMSP18A_P53 (SEQ ID NO:138), wherein said first amino acid sequenceand second amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMSP18A_P53 (SEQ IDNO:138), comprising a polypeptide having a length “n”, wherein n is atleast about 10 amino acids in length, optionally at least about 20 aminoacids in length, preferably at least about 30 amino acids in length,more preferably at least about 40 amino acids in length and mostpreferably at least about 50 amino acids in length, wherein at least twoamino acids comprise QD, having a structure as follows: a sequencestarting from any of amino acid numbers 89−x to 89; and ending at any ofamino acid numbers 90+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in F05068_P6 (SEQ ID NO:193), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-83 of ADML_HUMAN (SEQ ID NO:413), which also corresponds to aminoacids 1-83 of F05068_P6 (SEQ ID NO:193), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceCLSSPSPRPQQSGCRPHPSQALPPEHEQLPGPPELWLPLRDVHGAEAGTPDLPVHR (SEQ ID NO:490) corresponding to amino acids 84-139 of F05068_P6 (SEQ ID NO:193),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of F05068_P6 (SEQ ID NO:193), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceCLSSPSPRPQQSGCRPHPSQALPPEHEQLPGPPELWLPLRDVHGAEAGTPDLPVHR (SEQ ID NO:490) of F05068_P6 (SEQ ID NO:193).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in F05068_P9 (SEQ ID NO:194), comprisinga amino acid sequence being at least 90% homologous to amino acids 1-33of ADML_HUMAN (SEQ ID NO:413), which also corresponds to amino acids1-33 of F05068_P9 (SEQ ID NO:194).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in F05068_P10 (SEQ ID NO:195),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-82 of ADML_HUMAN (SEQ ID NO:413), which also correspondsto amino acids 1-82 of F05068_P10 (SEQ ID NO:195), and an amino acid R,wherein said first amino acid sequence and said amino acid arecontiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P6 (SEQ ID NO:215),comprising an amino acid sequence being at least 90% homologous to aminoacids 86-178 of IL10_HUMAN (SEQ ID NO:423), which also corresponds toamino acids 1-93 of HUMIL10_P6 (SEQ ID NO:215).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P6 (SEQ ID NO:215),comprising a first amino acid sequence being at least 90% homologous toamino acids 86-126 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 1-41 of HUMIL10_P6 (SEQ ID NO:215), abridging amino acid H corresponding to amino acid 42 of HUMIL10_P6 (SEQID NO:215), and a second amino acid sequence being at least 90%homologous to amino acids 128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545),which also corresponds to amino acids 43-93 of HUMIL10_P6 (SEQ IDNO:215), wherein said first amino acid sequence, bridging amino acid andsecond amino acid sequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P9 (SEQ ID NO:216),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MMPPACPLSVMDMELEARTNTFSFLPQ (SEQ ID NO: 584) corresponding toamino acids 1-28 of HUMIL10_P9 (SEQ ID NO:216), and a second amino acidsequence being at least 90% homologous to amino acids 127-178 ofIL10_HUMAN (SEQ ID NO:423), which also corresponds to amino acids 29-80of HUMIL10_P9 (SEQ ID NO:216), wherein said first amino acid sequenceand second amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMIL10_P9 (SEQ ID NO:216), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 584) of HUMIL10_P9 (SEQ IDNO:216).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P9 (SEQ ID NO:216),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 584) corresponding toamino acids 1-28 of HUMIL10_P9 (SEQ ID NO:216), and a second amino acidsequence being at least 90% homologous to amino acids 109-160 ofQ71UZ1_HUMAN (SEQ ID NO: 542), which also corresponds to amino acids29-80 of HUMIL10_P9 (SEQ ID NO:216), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P9 (SEQ ID NO:216),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MMPPACPLSVMDMELEARITNTFSFLPQH (SEQ ID NO: 585) corresponding toamino acids 1-29 of HUMIL10_P9 (SEQ ID NO:216), and a second amino acidsequence being at least 90% homologous to amino acids 128-178 ofQ6FGS9_HUMAN (SEQ ID NO: 545), which also corresponds to amino acids30-80 of HUMIL10_P9 (SEQ ID NO:216), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P10 (SEQ ID NO:217),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-50 of IL10_HUMAN (SEQ ID NO:423), which also correspondsto amino acids 1-50 of HUMIL10_P10 (SEQ ID NO:217), and a second aminoacid sequence being at least 90% homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 56-178 of IL10_HUMAN (SEQ ID NO:423), whichalso corresponds to amino acids 51-173 of HUMIL10_P10 (SEQ ID NO:217),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMIL10_P10 (SEQ ID NO:217),comprising a polypeptide having a length “n”, wherein n is at leastabout 10 amino acids in length, optionally at least about 20 amino acidsin length, preferably at least about 30 amino acids in length, morepreferably at least about 40 amino acids in length and most preferablyat least about 50 amino acids in length, wherein at least two aminoacids comprise RQ, having a structure as follows: a sequence startingfrom any of amino acid numbers 50−x to 50; and ending at any of aminoacid numbers 51+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P10 (SEQ ID NO:217),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-50 of Q6FGW4_HUMAN (SEQ ID NO: 543), which alsocorresponds to amino acids 1-50 of HUMIL10_P10 (SEQ ID NO:217), and asecond amino acid sequence being at least 90% homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 56-178 of Q6FGW4_HUMAN (SEQ ID NO: 543),which also corresponds to amino acids 51-173 of HUMIL10_P10 (SEQ IDNO:217), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P10 (SEQ ID NO:217),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-50 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 1-50 of HUMIL10_P10 (SEQ ID NO:217), a secondamino acid sequence being at least 90% homologous to amino acids 56-126of Q6FGS9_HUMAN (SEQ ID NO: 545), which also corresponds to amino acids51-121 of HUMIL10_P10 (SEQ ID NO:217), a bridging amino acid Hcorresponding to amino acid 122 of HUMIL10_P10 (SEQ ID NO:217), and athird amino acid sequence being at least 90% homologous to amino acids128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545), which also corresponds toamino acids 123-173 of HUMIL10_P10 (SEQ ID NO:217), wherein said firstamino acid sequence, second amino acid sequence, bridging amino acid andthird amino acid sequence are contiguous and in a sequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P10 (SEQ ID NO:217),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) corresponding to aminoacids 1-18 of HUMIL10_P10 (SEQ ID NO:217), a second amino acid sequencebeing at least 90% homologous to amino acids 1-32 of Q71UZ1_HUMAN (SEQID NO: 542), which also corresponds to amino acids 19-50 of HUMIL10_P10(SEQ ID NO:217), and a third amino acid sequence being at least 90%homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFNYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 38-160 of Q71UZ1_HUMAN (SEQ ID NO: 542),which also corresponds to amino acids 51-173 of HUMIL10_P10 (SEQ IDNO:217), wherein said first amino acid sequence, second amino acidsequence and third amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMIL10_P10 (SEQ ID NO:217), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMHSSALLCCLVLLTGVRA (SEQ ID NO: 586) of HUMIL10_P10 (SEQ ID NO:217).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P10 (SEQ ID NO:217),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-50 of Q6LBF4_HUMAN (SEQ ID NO: 546), which alsocorresponds to amino acids 1-50 of HUMIL10_P10 (SEQ ID NO:217), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 51-173 of HUMIL10_P10 (SEQ ID NO:217),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMIL10_P10 (SEQ ID NO:217), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491) ofHUMIL10_P10 (SEQ ID NO:217).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P12 (SEQ ID NO:218),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-126 of IL10_HUMAN (SEQ ID NO:423), which also correspondsto amino acids 1-126 of HUMIL10_P12 (SEQ ID NO:218), and a second aminoacid sequence being at least 90% homologous toLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding to amino acids 149-178 ofIL10_HUMAN (SEQ ID NO:423), which also corresponds to amino acids127-156 of HUMIL10_P12 (SEQ ID NO:218), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMIL10_P12 (SEQ ID NO:218),comprising a polypeptide having a length “n”, wherein n is at leastabout 10 amino acids in length, optionally at least about 20 amino acidsin length, preferably at least about 30 amino acids in length, morepreferably at least about 40 amino acids in length and most preferablyat least about 50 amino acids in length, wherein at least two aminoacids comprise CL, having a structure as follows: a sequence startingfrom any of amino acid numbers 126−x to 126; and ending at any of aminoacid numbers 127+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P12 (SEQ ID NO:218),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) corresponding to aminoacids 1-18 of HUMIL10_P12 (SEQ ID NO:218), a second amino acid sequencebeing at least 90% homologous to amino acids 1-108 of Q71UZ1_HUMAN (SEQID NO: 542), which also corresponds to amino acids 19-126 of HUMIL10_P12(SEQ ID NO:218), and a third amino acid sequence being at least 90%homologous to LQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding to aminoacids 131-160 of Q71UZ1_HUMAN (SEQ ID NO: 542), which also correspondsto amino acids 127-156 of HUMIL10_P12 (SEQ ID NO:218), wherein saidfirst amino acid sequence, second amino acid sequence and third aminoacid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMIL10_P12 (SEQ ID NO:218), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMHSSALLCCLVLLTGVRA (SEQ ID NO: 586) of HUMIL10_P12 (SEQ ID NO:218).

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMIL10_P12 (SEQ ID NO:218),comprising a polypeptide having a length “n”, wherein n is at leastabout 10 amino acids in length, optionally at least about 20 amino acidsin length, preferably at least about 30 amino acids in length, morepreferably at least about 40 amino acids in length and most preferablyat least about 50 amino acids in length, wherein at least two aminoacids comprise CL, having a structure as follows: a sequence startingfrom any of amino acid numbers 126−x to 126; and ending at any of aminoacid numbers 127+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P12 (SEQ ID NO:218),comprising a first amino acid sequence being at least 90% homologous toMHSSALLCCLVLLTGVRASPGQGTQSENSCTBFPGNLPNMLRDLRDAFSRVKTFF corresponding toamino acids 1-55 of Q6LBF4_HUMAN (SEQ ID NO: 546), which alsocorresponds to amino acids 1-55 of HUMIL10_P12 (SEQ ID NO:218), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 492) corresponding to aminoacids 56-156 of HUMIL10_P12 (SEQ ID NO:218), wherein said first aminoacid sequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptide asset forth in a tail of HUMIL10_P12 (SEQ ID NO:218), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 492) of HUMIL10_P12 (SEQ IDNO:218).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P13 (SEQ ID NO:219),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587) corresponding toamino acids 1-27 of HUMIL10_P13 (SEQ ID NO:219), and a second amino acidsequence being at least 90% homologous to amino acids 127-178 ofIL10_HUMAN (SEQ ID NO:423), which also corresponds to amino acids 28-79of HUMIL10_P13 (SEQ ID NO:219), wherein said first amino acid sequenceand second amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMIL10_P13 (SEQ ID NO:219), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587) of HUMIL10_P13 (SEQ IDNO:219).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMIL10_P13 (SEQ ID NO:219),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587) corresponding toamino acids 1-27 of HUMIL10_P13 (SEQ ID NO:219), and a second amino acidsequence being at least 90% homologous to amino acids 109-160 ofQ71UZ1_HUMAN (SEQ ID NO: 542), which also corresponds to amino acids28-79 of HUMIL10_P13 (SEQ ID NO:219), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in AA336074_P30 (SEQ ID NO:236),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-158 of KLK4_HUMAN (SEQ ID NO:430), which also correspondsto amino acids 1-158 of AA336074_P30 (SEQ ID NO:236), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceDAVIAIQSQTVGGWECEKLSQPWQGCTISATSSARTSCCILTGCSLLLTASPGVEIRRDSAGCSHMIKEGPELGVTPDPS (SEQ ID NO: 493) corresponding to amino acids 159-238 ofAA336074_P30 (SEQ ID NO:236), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of AA336074_P30 (SEQ ID NO:236), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceDAVIAIQSQTVGGWECEKLSQPWQGCTISATSSARTSCCILTGCSLLLTASPGVEIRRDSAGCSHMIKEGPELGVTPDPS (SEQ ID NO: 493) of AA336074_P30 (SEQ ID NO:236).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z39737_P9 (SEQ ID NO:307), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-136 of SPO2_HUMAN_V1, which also corresponds to amino acids 1-136 ofZ39737_P9 (SEQ ID NO:307), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequenceFLQQGCPPSPGVPTGFPGASYSATMWEFHHHRDLSGSSGSYVETRNSSP (SEQ ID NO: 494)corresponding to amino acids 137-185 of Z39737_P9 (SEQ ID NO:307),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z39737_P9 (SEQ ID NO:307), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceFLQQGCPPSPGVPTGFPGASYSATMWEFHHHRDLSGSSGSYVETRNSSP (SEQ ID NO: 494) ofZ39737_P9 (SEQ ID NO:307).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z25299_P1 (SEQ ID NO:345), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-131 of ALK1_HUMAN (SEQ ID NO:443), which also corresponds to aminoacids 1-131 of Z25299_P1 (SEQ ID NO:345), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence GKQGMRAH (SEQ ID NO:495) corresponding to amino acids 132-139 of Z25299_P1 (SEQ ID NO:345),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z25299_P1 (SEQ ID NO:345), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequence GKQGMRAH(SEQ ID NO: 495) of Z25299_P1 (SEQ ID NO:345).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z25299_P4 (SEQ ID NO:346), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-131 of ALK1_HUMAN (SEQ ID NO:443), which also corresponds to aminoacids 1-131 of Z25299_P4 (SEQ ID NO:346), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGCFSPSISPSHFFTMSSISTFSAVLRTSASSLSACVLPATHQMRSGEEFSTFGFMLVLK (SEQ ID NO:496) corresponding to amino acids 132-190 of Z25299_P4 (SEQ ID NO:346),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z25299_P4 (SEQ ID NO:346), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceGCFSPSISPSHFFTMSSISTFSAVLRTSASSLSACVLPATHQMRSGEEFSTFGFMLVLK (SEQ ID NO:496) of Z25299_P4 (SEQ ID NO:346).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z25299_P5 (SEQ ID NO:347), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-131 of ALK1_HUMAN (SEQ ID NO:443), which also corresponds to aminoacids 1-131 of Z25299_P5 (SEQ ID NO:347), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEKRHHKQLRDQEVDPLEMRRHSAG (SEQ ID NO: 497) corresponding to amino acids132-156 of Z25299_P5 (SEQ ID NO:347), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z25299_P5 (SEQ ID NO:347), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceGEKRHHKQLRDQEVDPLEMRRHSAG (SEQ ID NO: 497) of Z25299_P5 (SEQ ID NO:347).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z25299_P6 (SEQ ID NO:348), comprisinga first amino acid sequence being at least 90% homologous to amino acids1-81 of NP_(—)003055 (SEQ ID NO: 550), which also corresponds to aminoacids 1-81 of Z25299_P6 (SEQ ID NO:348), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence RGSLGSAQ (SEQ ID NO:498) corresponding to amino acids 82-89 of Z25299_P6 (SEQ ID NO:348),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z25299_P6 (SEQ ID NO:348), comprising anamino acid sequence being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequence RGSLGSAQ(SEQ ID NO: 498) of Z25299_P6 (SEQ ID NO:348).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z25299_P8 (SEQ ID NO:349), comprisinga amino acid sequence being at least 90% homologous to amino acids 1-82of ALK1_HUMAN (SEQ ID NO:443), which also corresponds to amino acids1-82 of Z25299_P8 (SEQ ID NO:349), wherein said and first amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of Z25299_P8 (SEQ ID NO:349),comprising a polypeptide having a length “n”, wherein n is at leastabout 10 amino acids in length, optionally at least about 20 amino acidsin length, preferably at least about 30 amino acids in length, morepreferably at least about 40 amino acids in length and most preferablyat least about 50 amino acids in length, wherein at least two aminoacids comprise T, having a structure as follows: a sequence startingfrom any of amino acid numbers 82−x to 82; and ending at any of aminoacid numbers 82+((n−2)−x), in which x varies from 0 to n−2. In someembodiments, the isolated chimeric proteins or polypeptides of theinvention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z22012_P41 (SEQ ID NO:254),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-125 of L3BP_HUMAN (SEQ ID NO: 441), which also correspondsto amino acids 1-125 of Z22012_P41 (SEQ ID NO:254), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 499) corresponding to aminoacids 126-156 of Z22012_P41 (SEQ ID NO:254), wherein said first aminoacid sequence and second amino acid sequence are contiguous and in asequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z22012_P41 (SEQ ID NO:254), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 499) of Z22012_P41 (SEQ IDNO:254).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z22012_P41 (SEQ ID NO:254),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRBERDAGVVCTNGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 589) corresponding to amino acids 126-156 ofZ22012_P41 (SEQ ID NO:254), and a second amino acid sequence being atleast 90% homologous to amino acids 1-125 of NP_(—)005558 (SEQ ID NO:551), which also corresponds to amino acids 1-125 of Z22012_P41 (SEQ IDNO:254), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of Z22012_P41 (SEQ ID NO:254), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 589) of Z22012_P41 (SEQ ID NO:254).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z22012_P42 (SEQ ID NO:255),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ IDNO: 590) corresponding to amino acids 126-205 of Z22012_P42 (SEQ IDNO:255), and a second amino acid sequence being at least 90% homologousto amino acids 1-125 of L3BP_HUMAN (SEQ ID NO: 441), which alsocorresponds to amino acids 1-125 of Z22012_P42 (SEQ ID NO:255), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of Z22012_P42 (SEQ ID NO:255), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ IDNO: 590) of Z22012_P42 (SEQ ID NO:255).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in Z22012_P42 (SEQ ID NO:255),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-125 of NP_(—)005558 (SEQ ID NO: 551), which alsocorresponds to amino acids 1-125 of Z22012_P42 (SEQ ID NO:255), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ ID NO: 500) corresponding to amino acids 126-205 ofZ22012_P42 (SEQ ID NO:255), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of Z22012_P42 (SEQ ID NO:255), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ ID NO: 500) of Z22012_P42 (SEQ ID NO:255).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMTREFAC_P9 (SEQ ID NO:245),comprising a first amino acid sequence being at least 90% homologous toamino acids 1-28 of TFF3_HUMAN (SEQ ID NO:440), which also correspondsto amino acids 1-28 of HUMTREFAC_P9 (SEQ ID NO:245), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECLGVSSPCRKQNAPSEAPPAAPGRGMRGSEBPCPAVIAARHCSSQLFCPFAPGKRFC (SEQ ID NO: 501) corresponding toamino acids 29-137 of HUMTREFAC_P9 (SEQ ID NO:245), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for an edge portion of HUMTREFAC_P9 (SEQ ID NO:245), comprisingan amino acid sequence being at least 70%, optionally at least about80%, preferably at least about 85%, more preferably at least about 90%and most preferably at least about 95% homologous to the sequenceQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECLGVSSPCRKQNAPSEAPPAAPGRGMRGSEHPCPAVIAARHCSSQLFCPFAPGKRFC (SEQ ID NO: 501) of HUMTREFAC_P9(SEQ ID NO:245).

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMTREFAC_P9 (SEQ ID NO:245),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequenceMAARALCMLGLVLALLSSSSAEEYVGLSQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECL (SEQ ID NO: 591) corresponding to amino acids 29-137 ofHUMTREFAC_P9 (SEQ ID NO:245), and a second amino acid sequence being atleast 90% homologous to ANQCAVPAKDRVDCGYPHVTPKE corresponding to aminoacids 51-78 of Q96NX0_HUMAN (SEQ ID NO: 554), which also corresponds toamino acids 1-28 of HUMTREFAC_P9 (SEQ ID NO:245), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

In some embodiments, this invention provides an isolated polypeptideencoding for a head of HUMTREFAC_P9 (SEQ ID NO:245), comprising apolypeptide being at least 70%, optionally at least about 80%,preferably at least about 85%, more preferably at least about 90% andmost preferably at least about 95% homologous to the sequenceMAARALCMLGLVLALLSSSSAEEYVGLSQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECL (SEQ ID NO: 591) of HUMTREFAC_P9 (SEQ ID NO:245).

In some embodiments, this invention provides an isolated chimericpolypeptide encoding for an edge portion of HUMTREFAC_P9 (SEQ IDNO:245), comprising a polypeptide having a length “n”, wherein n is atleast about 10 amino acids in length, optionally at least about 20 aminoacids in length, preferably at least about 30 amino acids in length,more preferably at least about 40 amino acids in length and mostpreferably at least about 50 amino acids in length, wherein at least twoamino acids comprise LG, having a structure as follows: a sequencestarting from any of amino acid numbers 137−x to 137; and ending at anyof amino acid numbers 1+((n−2)−x), in which x varies from 0 to n−2.

In some embodiments, the isolated chimeric proteins or polypeptides ofthe invention may comprise an amino acid sequence corresponding to orhomologous to that as set forth in HUMTREFAC_P9 (SEQ ID NO:245),comprising a first amino acid sequence being at least 70%, optionally atleast 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95%, homologous to a polypeptide having thesequenceMAARALCMLGLVLALLSSSSAEEYVGLSQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECLGVSSPCRKQNAPSEAPPAAPGRGMRGSEEPCPAVIAARHCSSQLFCPFAPGKRFC (SEQID NO: 592) corresponding to amino acids 29-137 of HUMTREFAC_P9 (SEQ IDNO:245), and a second amino acid sequence being at least 90% homologousto amino acids 51-78 of NP_(—)003217 (SEQ ID NO: 555), which alsocorresponds to amino acids 1-28 of HUMTREFAC_P9 (SEQ ID NO:245), whereinsaid, first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

In some embodiments, the term “polypeptide” is to be understood to referto a molecule comprising from at least 2 to several thousand or moreamino acids. The term “polypeptide” is to be understood to include,inter alia, native peptides (either degradation products, syntheticallysynthesized peptides or recombinant peptides), peptidomimetics, such aspeptoids and semipeptoids or peptide analogs, which may comprise, forexample, any desirable modification, including, inter alia,modifications rendering the peptides more stable while in a body or morecapable of penetrating into cells, or others as will be appreciated byone skilled in the art. Such modifications include, but are not limitedto N terminus modification, C terminus modification, peptide bondmodification, backbone modifications, residue modification, or others.Inclusion of such peptides within the polypeptides of this invention mayproduce a polypeptide sharing identity with the polypeptides describedherein, for example, those provided in the sequence listing.

Methods for preparing, isolating, deriving, etc., the polypeptides ofthis invention are well known are well known in the art. In someembodiments, the polypeptides of this invention comprise variants ofknown proteins. For example, and in some embodiments, the polypeptidesof this invention comprise splice variants of native proteins expressedin a given subject. In some embodiments, the polypeptides may beobtained through known protein evolution techniques available in theart. In some embodiments, the polypeptides of this invention may beobtained via rational design, based on a particular native polypeptidesequence.

In some embodiments, this invention provides for antibodies or antibodyfragments specifically interacting with or recognizing a polypeptide ofthis invention.

In one embodiment, the antibody recognizes one or more epitopes (antigendeterminants) contained within the polypeptides of this invention. Insome embodiments, reference to the antibody property of “specificinteraction” or “recognition” is to be understood as including covalentand non-covalent associations, and with a variance of affinity overseveral orders of magnitude. Such terms are to be understood asrelative, with respect to an index molecule, for which the antibody isthough to have little to no specific interaction or recognition.

In one embodiment, the antibodies will specifically interact orrecognize a particular antigen determinant. In some embodiments, theantibodies or antibody fragments of this invention will recognize orinteract with a polypeptide or protein of the invention, and will notsubstantially recognize or interact with other molecules, even whenpresent in the same sample, such as a biological sample. In someembodiments, the antibodies of this invention have a specificity suchthat the specific interaction with or binding to the antigen is at leastabout 2, or in some embodiments, at least about 5, or in someembodiments, at least about 10-fold greater than interaction or bindingobserved under the same reaction conditions with a molecule that doesnot include the antigenic determinant.

The antibodies may be useful, in some embodiments, in detectingqualitative and/or quantitative changes in expression of thepolypeptides or polynucleotides of this invention. In some embodiments,changes in expression are associated with a particular disease ordisorder, such that detection of such changes comprises a diagnosticmethod of this invention.

In one embodiment, this invention provides a diagnostic kit fordetecting a disease, comprising reagents which detect qualitative and/orquantitative changes in expression of a polypeptide or polynucleotide ofthis invention.

Optionally, the kit comprises a NAT-based technology; optionally andpreferably, the kit further comprises at least one nucleotide probe orprimer, alternatively and optionally this kit comprises at least oneprimer pair capable of selectively hybridizing to a nucleic acidsequence as described herein; alternatively and optionally, said kitfurther comprises at least one oligonucleotide capable of selectivelyhybridizing to a nucleic acid sequence according to any of the aboveclaims.

Alternatively and optionally, the kit comprises an antibody according toany of the above claims (optionally and preferably, the kit furthercomprises at least one reagent for performing an ELISA or a Westernblot.

In some embodiments, this invention provides a diagnostic method, forexample, a method of detection of a polypeptide or polynucleotide ofthis invention, whereby expression, or relative changes in expression ofthe polypeptide or polynucleotide herald the onset, severity, orprognosis of an individual with regard to a particular disease, disorderor condition.

In some embodiments, such detection may comprise detection of specificexpression of a splice variant, or other polypeptide or polynucleotideof this invention, via any means known in the art, and as describedherein. In some embodiments, detection of the following genes and/ortheir products is part of the diagnostic methods of this invention:HSFLT, HSI1RA, HSPLGF, HUMSP18A, F05068, HUMIL10, or any combinationthereof. In some embodiments, detection of these genes, or relativechanges in expression of the genes, their products or certain variantsthereof herald the onset, severity or prognosis of cardiovasculardisease in a subject. In some embodiments, the polypeptides,polynucleotides and/or methods of this invention may be useful in thetreatment, diagnosis or prognosis assessment of any cardiovasculardisease, including, inter alia, myocardial infarct, acute coronarysyndrome, coronary artery disease, angina pectoris (stable andunstable), cardiomyopathy, myocarditis, congestive heart failure or anytype of heart failure, reinfarction, assessment of thrombolytic therapy,assessment of myocardial infarct size, differential diagnosis betweenheart-related versus lung-related conditions (such as pulmonaryembolism), the differential diagnosis of Dyspnea, cardiac valves relatedconditions, vascular disease, or any combination thereof.

The polypeptides and/or polynucleotides of this invention may serve asmarkers or indicators of disease initiation, severity and/or response totreatment, for the indicated disease, disorder or condition, and theiruse as such is to be considered part of this invention, and part of themethods of this invention.

In some embodiments, detection of SFLT, HSI1RA, HSPLGF, HUMSP18A,F05068, HUMIL10, or any combination thereof, or relative changes inexpression of the genes, their products or certain variants thereofherald the onset, severity or prognosis of cerebrovascular disease in asubject. In some embodiments, the polypeptides, polynucleotides and/ormethods of this invention may be useful in the treatment, diagnosis orprognosis assessment of any cerebrovascular disease, including, interalia, stroke, including any type of stroke or neural tissue injury, orany type of cerebrovascular accident, ischemic stroke, hemorrhagicstroke or transient ischemic attacks, thrombotic, embolic, lacunar orhypoperfusion types of strokes, brain trauma, etc. In some embodiments,the polypeptides, polynucleotides and/or methods of this invention maybe useful in the establishment of the timing of stroke; the type ofstroke; the extent of tissue damage as a result of the stroke; responseto immediate treatments that are meant to alleviate the extent of strokeand brain damage, when available, or any combination thereof.

In some embodiments, the polypeptides, polynucleotides and/or methods ofthis invention may be useful in the diagnosis of stroke and indicationif an ischemic stroke has occurred; or a hemorrhagic stroke hasoccurred; or prognosis of a subsequent cerebral vasospasm; etc.

In some embodiments, the polypeptides, polynucleotides and/or methods ofthis invention may be useful in identifying a patient at risk forcerebral vasospasm. Such methods preferably comprise comparing an amountof one or more marker(s) predictive of a subsequent cerebral vasospasmin a test sample from a patient diagnosed with a subarachnoidhemorrhage. Such markers may be one or more markers related to bloodpressure regulation, markers related to inflammation, markers related toapoptosis, and/or specific markers of neural tissue injury.

In some embodiments, the polypeptides, polynucleotides and/or methods ofthis invention may be useful in the diagnosis, treatment or assessmentof the prognosis of a subject with cardiomyopathy and/or myocarditis,and/or related conditions as described herein. In some embodiments,markers utilized in this context are polynucleotides encoding orpolypeptides comprising HSFLT, HSI1Ra, HSPLGF, HUMSP18A, F05068 and/orHUMIL10 clusters, or variants thereof, or combinations thereof.

In some embodiments, the polypeptides, polynucleotides and/or methods ofthis invention may be useful in the diagnosis, treatment or assessmentof the prognosis of a subject with acute and chronic inflammation,and/or CVS diseases, and in some embodiments, the marker comprises oneor more of HSFLT variants, HSI1Ra variants, HSPLGF variants, HUMSP18Avariants, F05068 variants and/or HUMIL10 variants, including for aspectrum of diseases where an inflammatory process plays a substantialrole. In some embodiments, the polypeptides, polynucleotides and/ormethods of this invention may be useful in the diagnosis, treatment orassessment of the prognosis of a subject with hypercholesterolemia,diabetes, atherosclerosis, inflammation that involves bloodvessels—whether acute or chronic including but not limited to thecoronary arteries and blood vessels of the brain, myocardial infarction,cerebral stroke, peripheral vascular disease, vasculitis, polyarteritisnodosa, ANCA associated small vessel vasculitis, Churg-Strauss syndrome,Henoch-Schonlein purpura, scleroderma, thromboangiitis obliterans,temporal arteritis, Takayasu's arteritis, hypersensitivity vasculitis,Kawasaki disease, Behçet syndrome, and their complications including butnot limited to coronary disease, angina pectoris, deep vein thrombosis,renal disease, diabetic nephropathy, lupus nephritis, renal arterythrombosis, renal artery stenosis, atheroembolic disease of the renalarteries, renal vein thrombosis, hemolytic uremic syndrome, thromboticthrombocytopenic purpura, arteriolar nephrosclerosis, preeclampsia,eclampsia, albuminuria, microalbuminuria, glomerulonephritis, renalfailure, hypertension, uremia, cerebrovascular disease, peripheralvascular disease, intermittent claudication, abdominal angina;rheumatic/autoimmune diseases that involve systemic immune reactionincluding but not limited to rheumatoid arthritis, scleroderma, mixedconnective tissue disease, Sjogren syndrome, ankylosing spondylitis,spondyloarthropathy, psoriasis, psoriatic arthritis, myositis andsystemic lupus erythematosus; acute and/or chronic infective processesthat involve systemic immune reaction including but not limited topneumonia, bacteremia, sepsis, pyelonephritis, cellulitis,osteomyelitis, meningitis and viral hepatitis; malignant and idiopathicprocesses that involve systemic immune reaction and/or proliferation ofimmune cells including but not limited to granulomatous disorders,Wegener's granulomatosis, lymphomatoid granulomatosis/polymorphicreticulosis, idiopathic midline granuloma, multiple myeloma,Waldenstrom's macroglobulinemia, Castleman's disease, amyloidosis,lymphoma, histiocytosis, renal cell carcinoma and paraneoplasticsyndromes; conditions where CRP was shown to have a positive correlationwith the presence of the condition including but not limited to weightloss, anorexia-cachexia syndrome, extent of disease, recurrence inadvanced cancer, diabetes (types 1 & 2), obesity, hypertension, pretermdelivery; conditions which have similar symptoms, signs andcomplications as the conditions above and where the differentialdiagnosis between them and the conditions above is of clinicalimportance including but not limited to: other (non vascular) causes ofheart disease, renal disease and cerebral disease; other (non rheumatic)causes of arthropathy and musculoskeletal pain; other causes ofnon-specific symptoms and signs such as fever of unknown origin, loss ofappetite, weight loss, nonspecific pains, breathing difficulties,anxiety, or any combination thereof, or any disease disorder orcondition associated with inflammation.

In some embodiments, the polypeptides, polynucleotides and/or methods ofthis invention may be useful in the diagnosis, treatment or assessmentof the prognosis of a subject with congestive heart failure (CHF), andin some embodiments, the marker comprises a marker optionally selectedfrom the group consisting of one or more variants in HSFLT variants,HSI1Ra variants, HSPLGF variants, HUMSP18A variants, F05068 variantsand/or HUMIL10 variants or combinations thereof. In some embodiments,the polypeptides, polynucleotides and/or methods of this invention maybe useful in the diagnosis, treatment or assessment of the prognosis ofa subject with sudden cardiac death, from arrhythmia or any other heartrelated reason; rejection of a transplanted heart; conditions that leadto heart failure including but not limited to myocardial infarction,angina, arrhythmias, valvular diseases, atrial and/or ventricular septaldefects; conditions that cause atrial and or ventricular wall volumeoverload, including but not limited to systemic arterial hypertension,pulmonary hypertension and pulmonary embolism; conditions which havesimilar clinical symptoms as heart failure and as states that causeatrial and or ventricular pressure-overload, where the differentialdiagnosis between these conditions to the latter is of clinicalimportance including but not limited to breathing difficulty and/orhypoxia due to pulmonary disease, anemia or anxiety.

Each polypeptide or polynucleotide of the present invention describedherein may be used as a potential marker for cardiovascular conditions,might optionally be used alone or in combination with one or more othervariant markers described herein, and or in combination with knownmarkers for cardiovascular conditions, including but not limited toHeart-type fatty acid binding protein (H-FABP), Angiotensin, C-reactiveprotein (CRP), myeloperoxidase (MPO), and/or in combination with theknown protein(s) for the variant marker as described herein. Eachvariant marker of the present invention described herein as potentialmarker for cerebrovascular conditions, might optionally be used alone orin combination with one or more other variant markers described herein,and or in combination with known markers for cerebrovascular conditions,including but not limited to CRP, S100b, BNGF, CD40, MCP1,N-Acetyl-Aspartate (NAA), N-methyl-d-aspartate (NMDA) receptorantibodies (NR2Ab), and/or in combination with the known protein(s) forthe variant marker as described herein.

In some embodiments, the phrase “marker-detectable disease is aparticular cluster marker detectable disease” refers to the fact thatthe any polynucleotides and/or polypeptides of this invention can beused to detect the indicated disease, or assess the parameters of thedisease, etc., as described herein. In some embodiments, a particularcluster will be useful for the diagnosis, assessment and prognosticindications regarding the indicated disease disorder or condition.

In one embodiment, the marker-detectable disease is a cluster HSFLTmarker-detectable disease and is a cancer, including but not limited tocolon cancer, breast cancer, ovarian cancer, prostate cancer, or lungcancer.

In one embodiment, the marker-detectable disease is a cluster Z25299marker-detectable disease and is a cancer including but not limited tocolon cancer, breast cancer, ovarian cancer, lung cancer; and colon,breast, ovarian, and lung cancer invasion and metastasis.

In one embodiment, the marker-detectable disease is a cluster AA336074marker-detectable disease and is a cancer, including but not limited tobreast cancer, lung cancer; and breast and lung cancer invasion andmetastasis.

In one embodiment, the marker-detectable disease is a cluster HSPLGFmarker-detectable disease and is a variety of cancers, including but notlimited to colon cancer, lung cancer; and colon and lung cancer invasionand metastasis.

In one embodiment, the marker-detectable disease is a cluster HSI1RA,cluster HUMSP18A, cluster F05068 marker-detectable disease and is avariety of cancers, including but not limited to lung cancer and lungcancer invasion and metastasis.

In one embodiment, the marker-detectable disease is a cluster Z22012,cluster HUMTREFAC, or cluster Z39737 marker-detectable disease and is aprostate cancer.

With regard to lung cancer, the disease (and/or diagnostic method to beperformed) comprises, in some embodiments, one or more of invasive ormetastatic lung cancer; squamous cell lung carcinoma, lungadenocarcinoma, carcinoid, small cell lung cancer or non-small cell lungcancer; detection of overexpression in lung metastasis (vs. primarytumor); detection of overexpression in lung cancer, for example nonsmall cell lung cancer, for example adenocarcinoma, squamous cell canceror carcinoid, or large cell carcinoma; identification of a metastasis ofunknown origin which originated from a primary lung cancer; assessmentof a malignant tissue residing in the lung that is from a non-lungorigin, including but not limited to: osteogenic and soft tissuesarcomas; colorectal, uterine, cervix and corpus tumors; head and neck,breast, testis and salivary gland cancers; melanoma; and bladder andkidney tumors; distinguishing between different types of lung cancer,therefore potentially affect treatment choice (e.g. small cell vs. nonsmall cell tumors); analysis of unexplained dyspnea and/or chronic coughand/or hemoptysis; differential diagnosis of the origin of a pleuraleffusion; diagnosis of conditions which have similar symptoms, signs andcomplications as lung cancer and where the differential diagnosisbetween them and lung cancer is of clinical importance including but notlimited to: non-malignant causes of lung symptoms and signs, includingbut not limited to: lung lesions and infiltrates, wheeze, stridor,tracheal obstruction, esophageal compression, dysphagia, recurrentlaryngeal nerve paralysis, hoarseness, phrenic nerve paralysis withelevation of the hemidiaphragm and Horner syndrome; or detecting a causeof any condition suggestive of a malignant tumor including but notlimited to anorexia, cachexia, weight loss, fever, hypercalcemia,hypophosphatemia, hyponatremia, syndrome of inappropriate secretion ofantidiuretic hormone, elevated ANP, elevated ACTH, hypokalemia,clubbing, neurologic-myopathic syndromes and thrombophlebitis.

In some embodiments, the polypeptides and/or polynucleotides of thisinvention may be useful as potential markers for lung cancer, alone orin combination with one or more alternative polynucleotides orpolypeptides described herein, and/or in combination with known markersfor lung cancer, including but not limited to CEA, CA15-3,Beta-2-microglobulin, CA19-9, TPA, and/or in combination with the knownprotein(s) for the variant marker as described herein.

With regard to breast cancer, the disease (and/or diagnostic method tobe performed) the polypeptides, polynucleotides may be useful indetermining a probable outcome in breast cancer; detecting breast cancerin patients with age above 55 and/or patients with an age below 45;identification of a metastasis of unknown origin which originated from aprimary breast cancer tumor; assessing lymphadenopathy, and inparticular axillary lymphadenopathy; distinguishing between differenttypes of breast cancer, therefore potentially affect treatment choice(e.g. as HER-2); differentially diagnosing between a benign andmalignant breast mass; as a tool in the assessment of conditionsaffecting breast skin (e.g. Paget's disease) and their differentiationfrom breast cancer; differential diagnosis of breast pain or discomfortresulting from either breast cancer or other possible conditions (e.g.mastitis, Mondors syndrome); non-breast cancer conditions which havesimilar symptoms, signs and complications as breast cancer and where thedifferential diagnosis between them and breast cancer is of clinicalimportance including but not limited to: abnormal mammogram and/ornipple retraction and/or nipple discharge due to causes other thanbreast cancer, including but not limited to benign breast masses,melanoma, trauma and technical and/or anatomical variations; determininga cause of any condition suggestive of a malignant tumor including butnot limited to anorexia, cachexia, weight loss, fever, hypercalcemia,paraneoplastic syndrome; or determining a cause of lymphadenopathy,weight loss and other signs and symptoms associated with breast cancerbut originate from diseases different from breast cancer including butnot limited to other malignancies, infections and autoimmune diseases.

Each variant marker of the present invention described herein aspotential marker for breast cancer, might optionally be used alone or incombination with one or more other variant breast cancer describedherein, and/or in combination with known markers for breast cancer,including but not limited to Calcitonin, CA15-3 (Mucin1), CA27-29, TPA,a combination of CA 15-3 and CEA, CA 27.29 (monoclonal antibody directedagainst MUC1), Estrogen 2 (beta), HER-2 (c-erbB2), and/or in combinationwith the known protein(s) for the variant marker as described herein.

With regard to prostate cancer, the disease (and/or diagnostic method tobe performed) optionally and preferably comprises one or more ofinvasive or metastatic prostate cancer.

Each marker of the present invention described herein as potentialmarker for prostate cancer, might optionally be used alone or incombination with one or more other variant prostate cancer describedherein, and/or in combination with known markers for prostate cancer,including but not limited to PSA, PAP (prostatic acid phosphatase),CPK-BB, PSMA, PCA3, DD3, and/or in combination with the known protein(s)for the variant marker as described herein.

It is to be understood that any polynucleotide or polypeptide of thisinvention may be useful as a marker for a disease, disorder orcondition, and such use is to be considered a part of this invention.

With regard to colon cancer, the disease (and/or diagnostic method to beperformed) optionally and preferably comprises one or more of invasiveor metastatic colon cancer.

Each marker of the present invention described herein as potentialmarker for colorectal cancer, might optionally be used alone or incombination with one or more other variant colorectal cancer describedherein, and/or in combination with known markers for colorectal cancer,including but not limited to CEA, CA19-9, CA50, and/or in combinationwith the known protein(s) for the variant marker as described herein.

With regard to ovarian cancer, the polypeptides and/or polynucleotidemay be used in the diagnosis, treatment or prognostic assessment ofinvasive or metastatic ovarian cancer; correlating stage and malignantpotential; identification of a metastasis of unknown origin whichoriginated from a primary ovarian cancer, for example gastric carcinoma(such as Krukenberg tumor), breast cancer, colorectal carcinoma andpancreatic carcinoma; distinguishing between different types of ovariancancer, therefore potentially affect treatment choice (e.g.discrimination between epithelial tumors and germ cell tumors);differential diagnosis between benign and malignant ovarian cysts;diagnosing a cause of infertility, for example differential diagnosis ofvarious causes thereof; detecting of one or more non-ovarian cancerconditions that may elevate serum levels of ovary related markers,including but not limited to: cancers of the endometrium, cervix,fallopian tubes, pancreas, breast, lung and colon; nonmalignantconditions such as pregnancy, endometriosis, pelvic inflammatory diseaseand uterine fibroids; diagnosing conditions which have similar symptoms,signs and complications as ovarian cancer and where the differentialdiagnosis between them and ovarian cancer is of clinical importanceincluding but not limited to: non-malignant causes of pelvic mass,including, but not limited to: benign (functional) ovarian cyst, uterinefibroids, endometriosis, benign ovarian neoplasms and inflammatory bowellesions; determining a cause of any condition suggestive of a malignanttumor including but not limited to anorexia, cachexia, weight loss,fever, hypercalcemia, skeletal or abdominal pain, paraneoplasticsyndrome, or ascites.

In some embodiments, the polypeptides and/or polynucleotides of thisinvention may be used in the diagnosis, treatment or prognosticassessment of ovarian cancer, alone or in combination with one or morepolypeptides and/or polynucleotides of this invention, and/or incombination with known markers for ovarian cancer, including but notlimited to CEA, CA125 (Mucin 16), CA72-4TAG, CA-50, CA 54-61, CA-195 andCA 19-9 in combination with CA-125, and/or in combination with the knownprotein(s) associated with the indicated polypeptide or polynucleotide,as described herein.

Detecting specific expression may in some embodiments be performed witha NAT-based technology (optionally comprising at least one nucleotideprobe or primer), and/or with an immunoassay (optionally comprising anantibody according to any of the embodiments described herein).

In some embodiments, this invention provides a method of detecting,treating and/or assessing prognosis of a disease, disorder or condition,comprising detecting polypeptides and/or polynucleotides of thisinvention. In some embodiments, such methods are also referred to hereinas methods of screening for variant-detectable disease, whereby thedetection of variant expression serves as an indicator for the disease.In some embodiments, such detection may make use of a biomarker,antibody or any method or assay as described herein.

In some embodiments, this invention provides a method for screening fora disease, comprising detecting expression of:

-   -   a. a polypeptide having an amino acid sequence as set forth in        SEQ ID NOs: 16-31, 65-70, 99-102, 127-138, 215-219, 236, 245,        254-255, 307-308 or a homologue or fragment thereof;    -   b. a polypeptide comprising a bridge, edge portion, tail, or        head portion, wherein said polypeptide has an amino acid        sequence as set forth in SEQ ID NOs:459-501, 576-592 or a        homologue or fragment thereof;    -   c. a polynucleotide having a nucleic acid sequence as set forth        in SEQ ID NOs: 1-15, 61-64, 96-98, 114-126, 189-195, 211-214,        235, 244, 152-253, 305-306, 340-344. or a homologue or fragment        thereof;    -   d. a polynucleotide comprising a node having a nucleic acid        sequence as set forth in SEQ ID NOs: 32-60, 71-95, 103-113,        139-188, 196-219, 220-234, 237-243, 246-251, 256-304, 309-339,        350-358, 502-530;    -   e. an antibody capable of specifically binding to at least one        epitope of a polypeptide comprising an amino acid sequence as        set forth in SEQ ID NOs: 16-31, 65-70, 99-102, 127-138, 215-219,        236, 245, 254-255, 307-308, 459-501, 576-592;    -   f. an oligonucleotide having a nucleic acid sequence as set        forth in SEQ ID NOs:363, 383, 386, 389, 393, 396, 399, 407, 410,        414, 417, 420, 424, 427, 431, 434, 437, 444, 447, 452, 455, 458;    -   g. a primer pair, comprising a pair of isolated oligonucleotides        capable of specifically hybridizing to at least a portion of a        polynucleotide having a nucleic acid sequence as set forth in        SEQ ID NOs: 363, 383, 386, 389, 393, 396, 399, 407, 410, 414,        417, 420, 424, 427, 431, 434, 437, 444, 447, 452, 455; or        homologous thereto;    -   h. a primer pair, comprising a pair of isolated oligonucleotides        capable of specifically hybridizing to at least a portion of a        polynucleotide having a nucleic acid sequence as set forth in        SEQ ID NOs:361-362; 384-385; 387-388; 390-391; 394-395; 397-398;        400-401; 408-409; 411-412; 415-416; 418-419; 421-422; 425-426;        428-429; 432-433; 435-436; 438-439; 445-446; 448-449; 453-454;        456-457,        whereby qualitative or quantitative differences in expression as        compared to an index sample is indicator for the treatment,        diagnosis or assessment of prognosis of the disease, disorder or        condition.

In some embodiments, a method of this invention may make use of apolynucleotide, polypeptide, vector, antibody, biomarker, or combinationthereof, as described herein, including any embodiments thereof.

In some embodiments, the methods of this invention may be conducted on acell or tissue or body fluid sample isolated from a subject having,predisposed to, or suspected of having the disease disorder orcondition. In some embodiments, the methods are directed to themonitoring of disease progression and/or treatment efficacy and/orrelapse of the indicated disease, disorder or condition.

In another embodiment, this invention provides methods for the selectionof a particular therapy, or optimization of a given therapy for adisease, disorder or condition, the method comprising quantitativelyand/or qualitatively determining or assessing expression of thepolypeptides and/or polynucleotides, whereby differences in expressionfrom an index sample, or a sample taken from a subject prior to theinitiation of the therapy, or during the course of therapy, isindicative of the efficacy, or optimal activity of the therapy.

In some embodiments, for the polypeptides and/or polynucleotides of thisinvention are useful in applications in cardiac disease, as described,and provide for sensitive and accurate assessment. Biomolecularsequences (amino acid and/or nucleic acid sequences) uncovered using themethodology of the present invention and described herein can beutilized, in some embodiments, as tissue or pathological markers and/oras drugs or drug targets for treating preventing, diagnosing orassessing a disease.

In some embodiments, these markers are specifically released to thebloodstream under conditions of cardiac disease and/or cardiacpathology, as described herein. presenting some embodiments, thisinvention identified, or provides the means to identify clusters (genes)which are characterized in that their transcripts are differentiallyexpressed in heart muscle tissue compared with other normal tissues, forexample, in comparison to skeletal muscle tissue. In acute conditionsunder which heart muscle tissue experiences hypoxia (with or withoutnecrosis), intracellular proteins that are not normally secreted canleak through the cell membrane to the extracellular space. Therefore,heart muscle tissue differentially expresses proteins, and analysismethods as described herein may herald acute heart damage, therebyserving as cardiac disease markers.

In some embodiments, the identification/detection of the polypeptidesand/or polynucleotides of this invention signify leakage ofintracellular content, which can occur in chronic damage to the heartmuscle, therefore proteins selected according to this method arepotential markers for chronic heart conditions. When a protein that isdifferentially expressed in heart muscle is secreted, it may proveuseful as a chronic heart damage marker, since secretion implies thatthe protein has a physiological role exterior to the cell, and in someembodiments may be used by the heart muscle to respond to the chronicdamage.

In some embodiments, the markers described herein are overexpressed inheart versus skeletal muscle.

In some embodiments this invention provides diagnostic assays forcardiac disease and/or cardiac pathology, including but not limited tocardiac damage, and methods of use of such markers for detection ofcardiac disease and/or cardiac pathology, including but not limited tocardiac damage (alone or in combination), involving detection, in someembodiments of expression in a sample taken from a subject (patient),which in some embodiments, is a blood sample.

In some embodiments, the polypeptides and polynucleotides and methods ofthis invention find application in various cardiovascular andcerebrovascular conditions, and in some embodiments, the conditions mayalso optionally include stroke and various cardiomyopathies.

In some embodiments, the marker-detectable disease involves clusterZ25299 and comprises a variety of cancers, including but not limited tocolon cancer, breast cancer, ovarian cancer, lung cancer; and colon,breast, ovarian, and lung cancer invasion and metastasis.

In some embodiments, the marker-detectable disease involves clusterAA336074 and comprises a variety of cancers, including but not limitedto breast cancer, lung cancer; and breast and lung cancer invasion andmetastasis.

In some embodiments, the marker-detectable disease involves clusterHSPLGF and comprises a variety of cancers, including but not limited tocolon cancer, lung cancer; and colon and lung cancer invasion andmetastasis.

In some embodiments, the marker-detectable disease involves clusterHSI1RA, cluster HUMSP18A, cluster F05068 and comprises a variety ofcancers, including but not limited to lung cancer and lung cancerinvasion and metastasis.

In some embodiments, the marker-detectable disease involves clusterZ22012, cluster HUMTREFAC, or cluster Z39737 and comprises prostatecancer.

According to some embodiments of the present invention, any of the abovenucleic acid and/or amino acid sequences further comprises any sequencehaving at least about 70%, at least about 80%, at least about 90%, leastabout 95% homology to the polynucleotides herein described.

The nucleic acid sequences and/or amino acid sequences shown herein asembodiments of the present invention relate, in some embodiments, totheir isolated form, as isolated polynucleotides (including for alltranscripts), oligonucleotides (including for all segments, ampliconsand primers), peptides (including for all tails, bridges, insertions orheads, optionally including other antibody epitopes as described herein)and/or polypeptides (including for all proteins). It should be notedthat the terms “oligonucleotide” and “polynucleotide”, or “peptide” and“polypeptide”, may optionally be used interchangeably.

All technical and scientific terms used herein should be understood tohave the meaning commonly understood by a person skilled in the art towhich this invention belongs, as well as any other specifieddescription. The following references provide one of skill with ageneral definition of many of the terms used in this invention:Singleton et al., Dictionary of Microbiology and Molecular Biology (2nded. 1994); The Cambridge Dictionary of Science and Technology (Walkered., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.),Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionaryof Biology (1991). All of these are hereby incorporated by reference asif fully set forth herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is herein described, by way of example only, withreference to the accompanying drawings. With specific reference now tothe drawings in detail, it is stressed that the particulars shown are byway of example and for purposes of illustrative discussion of theembodiments of the present invention only, and are presented in thecause of providing what is believed to be the most useful and readilyunderstood description of the principles and conceptual aspects of theinvention. In this regard, no attempt is made to show structural detailsof the invention in more detail than is necessary for a fundamentalunderstanding of the invention, the description taken with the drawingsmaking apparent to those skilled in the art how the several forms of theinvention may be embodied in practice.

In the drawings:

FIG. 1: Schematic description of the cancer biomarker selection engine;

FIG. 2: Schematic illustration, depicting grouping of transcripts of agiven cluster based on presence or absence of unique sequence regions;

FIG. 3 shows the schematic summary of quantitative real-time PCRanalysis;

FIG. 4 shows the structure of the HSFLT variants mRNA and protein. Exonsare represented by white boxes, while introns are represented by twoheaded arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 5 shows expression of Homo sapiens fins-related tyrosine kinase 1(vascular endothelial growth factor/vascular permeability factorreceptor) (FLT1) transcripts detectable by or according toseg20—HSFLT_seg20 (SEQ ID NO:363) amplicon and primers HSFLT_seg20F (SEQID NO:361) and HSFLT_seg20R (SEQ ID NO:362) on a normal panel;

FIG. 6 shows the structure of the HSI1RA mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 7 is a histogram showing over expression of the Homo sapiensinterleukin 1 receptor antagonist (IL1RN) HSI1RA transcripts which aredetectable by amplicon as depicted in sequence name HSI1RA_junc15-17(SEQ ID NO:376) in normal and cancerous Lung tissues;

FIG. 8 shows expression of Homo sapiens interleukin 1 receptorantagonist (IL1RN) HSI1RA transcripts which are detectable by ampliconas depicted in sequence name HSI1RA_junc15-17 (SEQ ID NO:376) indifferent normal tissues;

FIG. 9 is a histogram showing down regulation of the above-indicatedHomo sapiens interleukin 1 receptor antagonist (IL1RN) transcripts incancerous lung samples relative to the normal samples (junc23-30);

FIG. 10 shows expression of Homo sapiens interleukin 1 receptorantagonist (IL1RN) HSI1RA transcripts which are detectable by ampliconas depicted in sequence name HSI1RA_junc23-30 (SEQ ID NO: 383) indifferent normal tissues;

FIGS. 11A and 11B are histograms showing down regulation of theabove-indicated Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts in cancerous lung samples relative to the normal samples(seg 23-24);

FIG. 12 shows expression of Homo sapiens interleukin 1 receptorantagonist (IL1RN) HSI1RA transcripts which are detectable by ampliconas depicted in sequence name HSI1RA_seg23-24 (SEQ ID NO: 386) indifferent normal tissues;

FIGS. 13A and 13B are histograms showing down regulation of theabove-indicated Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts in cancerous lung samples relative to the normal samples(seg 36-37);

FIG. 14 shows expression of Homo sapiens interleukin 1 receptorantagonist (IL1RN) HSI1RA transcripts which are detectable by ampliconas depicted in sequence name HSI1RA_seg36-37WT (SEQ ID NO: 389) indifferent normal tissues;

FIG. 15 shows the structure of the HSPLGF mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 16 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PLGF) transcripts in cancerous Lung samplesrelative to the normal samples;

FIG. 17 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg7WT (SEQ ID NO: 393) in different normal tissues;

FIG. 18 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PlGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg15-16 (SEQ ID NO:396) in different normal tissues;

FIG. 19 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) transcripts in cancerous Lung samplesrelative to the normal samples (seg16-21);

FIG. 20 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) transcripts in cancerous colon samplesrelative to the normal samples (seg16-21);

FIG. 21 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PlGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg16-21 (SEQ ID NO:399) in different normal tissues;

FIG. 22 shows the structure of the mRNA and protein variants of clusterHUMSP18A;

FIG. 23 is a histogram showing down regulation of the above-indicatedHomo sapiens surfactant, pulmonary-associated protein B (SFTPB),transcript variant 2 transcripts (seg32) in cancerous lung samplesrelative to the normal samples;

FIG. 24 shows expression of Homo sapiens surfactant,pulmonary-associated protein B (SFTPB) transcripts detectable by oraccording to seg32 in normal tissues;

FIG. 25 is a histogram showing down regulation of the above-indicatedHomo sapiens surfactant, pulmonary-associated protein B (SFTPB),transcript variant 2 transcripts in cancerous lung samples relative tothe normal samples (seg34-38WT);

FIG. 26 shows the results of expression of Homo sapiens surfactant,pulmonary-associated protein B (SFTPB) transcripts detectable by oraccording to seg34-38WT on a normal panel;

FIG. 27 shows cancer and cell-line vs. normal tissue expression forcluster F05068;

FIG. 28 shows the structure of the F05068 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 29 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068_seg3-5 (SEQ ID NO: 414) in different normal tissues;

FIG. 30 is a histogram showing down regulation of the above-indicatedHomo sapiens adrenomedullin (ADM) transcripts in cancerous lung samplesrelative to the normal samples (seg9);

FIG. 31 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068_seg9 (SEQ ID NO: 417) in different normal tissues;

FIG. 32 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068_seg13_WT (SEQ ID NO:420) in different normal tissues;

FIG. 33 is a histogram showing the expression of Homo sapiensadrenomedullin (ADM) F05068 transcripts which are detectable by ampliconas depicted in sequence name F05068_seg3-5 (SEQ ID NO: 414) in normaland cancerous Lung tissues.

FIG. 34 shows the structure of the HUMIL10 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIGS. 35A and 35B show expression of Homo sapiens interleukin 10 (IL10)transcripts detectable by or according to seg5, with the value ofrelative expression of each sample relative to median of the heartsamples as shown in FIG. 35A, or with the value of relative expressionof each sample relative to median of the blood samples as shown in FIG.35B;

FIGS. 36A and 36B show expression of Homo sapiens interleukin 10 (IL10)transcripts detectable by or according to seg0WT, with the value ofrelative expression of each sample relative to median of the heartsamples as shown in FIG. 36A, or with the value of relative expressionof each sample relative to median of the blood samples as shown in FIG.36B;

FIG. 37 shows that cluster AA336074 is overexpressed (at least at aminimum level) in the following pathological conditions: prostatecancer, a mixture of malignant tumors from different tissues andepithelial malignant tumors;

FIG. 38 shows the structure of the AA336074 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 39 is a histogram showing Expression of Homo sapiens kallikrein 4((KLK4) AA336074 transcripts which are detectable by amplicon asdepicted in sequence name AA336074_junc9-28 (SEQ ID NO:431) in normaland cancerous Breast tissues.

FIG. 40 is a histogram showing the expression of Homo sapiens kallikrein4 (KLK4) AA336074 transcripts which are detectable by amplicon asdepicted in sequence name AA336074_junc9-28 (SEQ ID NO:431) in differentnormal tissues.

FIG. 41 is a histogram showing Expression of Homo sapiens kallikrein 4((KLK4) AA336074 transcripts which are detectable by amplicon asdepicted in sequence name AA336074_seg13WT (SEQ ID NO:434) in normal andcancerous Breast tissues.

FIG. 42 is a histogram showing over expression of the Homo sapienskallilrein 4 (KLK4) AA336074 transcripts which are detectable byamplicon as depicted in sequence name AA336074_seg13WT (SEQ ID NO:434)in different normal tissues.

FIG. 43 is a histogram showing over expression of the Homo sapienskallikrein 4 (KLK4) AA336074 transcripts which are detectable byamplicon as depicted in sequence name AA336074 junc 9-28 (SEQ ID NO:431) in normal and cancerous lung tissues.

FIG. 44 is a histogram showing over expression of the Homo sapienskallikrein 4 (KLK4) AA336074 transcripts which are detectable byamplicon as depicted in sequence name AA336074 seg31 (SEQ ID NO: 437) innormal and cancerous breast tissues.

FIG. 45 is a histogram showing over expression of the Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) AA336074transcripts which are detectable by amplicon as depicted in sequencename AA336074_seg31 (SEQ ID NO:437) in different normal tissues.

FIG. 46 shows that cluster HUMTREFAC is overexpressed (at least at aminimum level) in the following pathological conditions: a mixture ofmalignant tumors from different tissues, pancreas carcinoma, prostatecancer, breast malignant tumors and epithelial malignant tumors;

FIG. 47 shows mRNA and protein structure of HUMTREFAC variants. Exonsare represented by white boxes, while introns are represented by twoheaded arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

FIG. 48 shows that cluster Z22012 is overexpressed (at least at aminimum level) in the following pathological conditions: brain malignanttumors, pancreas carcinoma, hepatocellular carcinoma, prostate cancer, amixture of malignant tumors from different tissues and myosarcoma;

FIG. 49 shows that cluster Z39737 is overexpressed (at least at aminimum level) in the following pathological conditions: prostatecancer.

FIG. 50 shows mRNA and Protein Structure of Z39737 variants. Exons arerepresented by white boxes, while introns are represented by two headedarrows. Proteins are shown in boxes with upper right to lower left fill.The unique regions are represented by white boxes with dashed frame.

FIG. 51—shows a graph of cancer and cell-line vs. normal tissueexpression for Z25299.

FIG. 52 shows mRNA and Protein Structure of Z25299 variants. Exons arerepresented by white boxes, while introns are represented by two headedarrows. Proteins are shown in boxes with upper right to lower left fill.The unique regions are represented by white boxes with dashed frame.

FIG. 53 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_junc13-14-21 (SEQ ID NO:444) in different normal tissues.

FIG. 54 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg12-13WT (SEQ ID NO: 447) in different normal tissues.

FIGS. 55-56 are histograms showing down regulation of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299_seg12-13WT (SEQ ID NO: 447) in cancerous lung samplesrelative to the normal samples.

FIG. 57 is a histogram showing over expression of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299_seg12-13WT (SEQ ID NO: 447) in cancerous Ovary samplesrelative to the normal samples.

FIGS. 58 and 59 are histograms showing down regulation of the Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts, which are detectable by amplicon as depicted in sequencename Z25299 seg20 (SEQ ID NO: 452) in cancerous lung samples relative tothe normal samples.

FIG. 60 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg20 (SEQ ID NO: 452) in different normal tissues.

FIG. 61 is a histogram showing over expression of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299_seg23 (SEQ ID NO: 455) in cancerous colon samples relativeto the normal samples.

FIG. 62 is a histogram showing down regulation of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299_seg23 (SEQ ID NO: 455) in cancerous lung samples relative tothe normal samples.

FIG. 63 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg23 (SEQ ID NO: 455) in different normal samples.

FIG. 64 is a histogram showing over expression of Z25299_junc13-14-21(SEQ ID NO: 444) transcripts in cancerous ovary samples relative to thenormal samples.

FIG. 65 is a histogram showing over expression of Z25299 seg20 (SEQ IDNO: 452) transcripts in cancerous ovary samples relative to the normalsamples.

FIG. 66 is a histogram showing over expression of Z25299 seg23 (SEQ IDNO: 455) transcripts in cancerous ovary samples relative to the normalsamples.

FIG. 67 is a histogram showing down regulation of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299_junc13-14-21 (SEQ ID NO: 444) in cancerous lung tissuesrelative to the normal samples.

FIG. 68 is a histogram showing over expression of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299 seg20 (SEQ ID NO: 452) in cancerous Colon tissues relativeto the normal samples.

FIG. 69 is a histogram showing down regulation of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299 seg20 (SEQ ID NO: 452) in cancerous breast tissues relativeto the normal samples.

FIG. 70 is a histogram showing down regulation of the Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) Z25299transcripts which are detectable by amplicon as depicted in sequencename Z25299 seg23 (SEQ ID NO: 455) in cancerous breast tissues relativeto the normal samples.

DESCRIPTION OF EMBODIMENTS

The present invention provides, in some embodiments, polynucleotides andpolypeptides and uses thereof, as further described herein.polynucleotides and polypeptides described herein, in some embodiments,represent variants, which may optionally be used as diagnostic markers.

In some embodiments, these variants are useful as diagnostic markers forcertain diseases, and as such the term “marker-detectable” or“variant-detectable” with regard to diseases is to be understood asencompassing use of the described polynucleotides and/or polypeptides.

In some embodiments, certain diseases are associated with differentialexpression, qualitatively or quantitatively, of the polynucleotides andpolypeptides of this invention. Assessment of such expression, in turn,may in some embodiments, serve as a marker for a particular diseasestate, susceptibility, pathogenesis, etc., including any desireddisease-specific event, whose analysis is useful, as will be appreciatedby one skilled in the art. In one embodiment, such use as a marker isalso referred to herein as the polynucleotides and polypeptides being“variant disease markers”.

The polynucleotides and polypeptides of the present invention, alone orin combination, in some embodiments, can be used for, and in someembodiments are a part of the methods of prognosis, prediction,screening, early diagnosis, staging, therapy selection and treatmentmonitoring of a marker-detectable disease. For example, in someembodiments, these markers may be used for the staging of disease in apatient (for example if the disease features cancer) and/or monitoringthe progression of the disease. Furthermore, the markers of the presentinvention, alone or in combination, can be used for detection of thesource of metastasis found in anatomical places other than theoriginating tissue, again in the example of cancer. Also, one or more ofthe markers may optionally be used in combination with one or more otherdisease markers (other than those described herein).

Biomolecular sequences (amino acid and/or nucleic acid sequences)uncovered using the methodology of the present invention and describedherein can be efficiently utilized, in some embodiments, as tissue orpathological markers and/or as drugs or drug targets for treating orpreventing a disease.

In some embodiments, these markers are released to the bloodstream underconditions of a particular disease, and/or are otherwise expressed at amuch higher level and/or specifically expressed in tissue or cellsafflicted with or demonstrating the disease. In some embodiments, themeasurement of these markers, alone or in combination, in patientsamples provides information that the diagnostician can correlate with aprobable diagnosis of a particular disease and/or a condition that isindicative of a higher risk for a particular disease.

The present invention provides, in some embodiments, diagnostic assaysfor a marker-detectable disease and/or an indicative condition, andmethods of use of such markers for detection of marker-detectabledisease and/or an indicative condition, for example in a sample takenfrom a subject (patient), which in some embodiments, is a blood sample.

Some embodiments of this invention have been exemplified herein whereincellular localization was determined via the use of four differentsoftware programs: (i) tmhmm (from Center for Biological SequenceAnalysis, Technical University of Denmark DTU,www.cbs.dtu.dk/services/TMHMM/TMHMM2.0b.guide.php) or (ii) tmpred (fromEMBnet, maintained by the ISREC Bioinformatics group and the LICRInformation Technology Office, Ludwig Institute for Cancer Research,Swiss Institute of Bioinformatics,www.ch.embnet.org/software/TMPRED_form.html) for transmembrane regionprediction; (iii) signalp_hmm or (iv) signalp_nn (both from Center forBiological Sequence Analysis, Technical University of Denmark DTU,www.cbs.dtu.dk/services/SignalP/background/prediction.php) for signalpeptide prediction. The terms “signalp_hmm” and “signalp_nn” refer totwo modes of operation for the program SignalP: hmm refers to HiddenMarkov Model, while nn refers to neural networks. Localization was alsodetermined through manual inspection of known protein localizationand/or gene structure, and the use of heuristics by the individualinventor. In some cases for the manual inspection of cellularlocalization prediction inventors used the ProLoc computational platform[Einat Hazkani-Covo, Erez Levanon, Galit Rotman, Dan Graur and AmitNovik; (2004) “Evolution of multicellularity in metazoa: comparativeanalysis of the subcellular localization of proteins in Saccharomyces,Drosophila and Caenorhabditis.” Cell Biology International 2004;28(3):171-8.], which predicts protein localization based on variousparameters including, protein domains (e.g., prediction oftrans-membranous regions and localization thereof within the protein),pI, protein length, amino acid composition, homology to pre-annotatedproteins, recognition of sequence patterns which direct the protein to acertain organelle (such as, nuclear localization signal, NLS,mitochondria localization signal), signal peptide and anchor modelingand using unique domains from Pfam that are specific to a singlecompartment.

Information is given in the text with regard to SNPs (single nucleotidepolymorphisms). A description of the abbreviations is as follows.“T->C”, for example, means that the SNP results in a change at theposition given in the table from T to C. Similarly, “M->Q”, for example,means that the SNP has caused a change in the corresponding amino acidsequence, from methionine (M) to glutamine (Q). If, in place of a letterat the right hand side for the nucleotide sequence SNP, there is aspace, it indicates that a frameshift has occurred. A frameshift mayalso be indicated with a hyphen (-). A stop codon is indicated with anasterisk at the right hand side (*). As part of the description of anSNP, a comment may be found in parentheses after the above descriptionof the SNP itself. This comment may include an FTId, which is anidentifier to a SwissProt entry that was created with the indicated SNP.An FTId is a unique and stable feature identifier, which allowsconstruction of links directly from position-specific annotation in thefeature table to specialized protein-related databases. The FTId isalways the last component of a feature in the description field, asfollows: FTId=XXX_number, in which XXX is the 3-letter code for thespecific feature key, separated by an underscore from a 6-digit number.In the table of the amino acid mutations of the wild type proteins ofthe selected splice variants of the invention, the header of the firstcolumn is “SNP position(s) on amino acid sequence”, representing aposition of a known mutation on amino acid sequence. SNPs may optionallybe used as diagnostic markers according to the present invention, aloneor in combination with one or more other SNPs and/or any otherdiagnostic marker. Embodiments of the present invention comprise suchSNPs, including but not limited to novel SNPs on the known (WT or wildtype) protein sequences given below, as well as novel nucleic acidand/or amino acid sequences formed through such SNPs, and/or any SNP ona variant amino acid and/or nucleic acid sequence described herein.

Some embodiments of this invention have been exemplified herein whereinhomology to known proteins was determined by Smith-Waterman version5.1.2 using special (non default) parameters as follows:

model=sw.model

GAPEXT=0

GAPOP=100.0

-   -   MATRIX=blosum100

Some embodiments of this invention have been exemplified herein whereinoverexpression of a cluster in cancer was a determination based on ESTs.A key to the p values with regard to the analysis of such overexpressionis as follows:

-   -   library-based statistics: P-value without including the level of        expression in cell-lines (P1)    -   library based statistics: P-value including the level of        expression in cell-lines (P2)    -   EST clone statistics: P-value without including the level of        expression in cell-lines (SP1)    -   EST clone statistics: predicted overexpression ratio without        including the level of expression in cell-lines (R3)    -   EST clone statistics: P-value including the level of expression        in cell-lines (SP2)    -   EST clone statistics: predicted overexpression ratio including        the level of expression in cell-lines (R4)

Library-based statistics refer to statistics over an entire library,while EST clone statistics refer to expression only for ESTs from aparticular tissue or cancer.

Some embodiments of this invention have been exemplified herein whereinoverexpression of a cluster in cancer was a determination based onmicroarray use. As a microarray reference, in the specific segmentparagraphs, the unabbreviated tissue name was used as the reference tothe type of chip for which expression was measured. There are two typesof microarray results: those from microarrays prepared according to adesign by the present inventors, for which the microarray fabricationprocedure is described in detail in Materials and ExperimentalProcedures section herein; and those results from microarrays usingAffymetrix technology. As a microarray reference, in the specificsegment paragraphs, the unabbreviated tissue name was used as thereference to the type of chip for which expression was measured. Formicroarrays prepared according to a design by the present inventors, theprobe name begins with the name of the cluster (gene), followed by anidentifying number. Oligonucleotide microarray results taken fromAffymetrix data were from chips available from Affymetrix Inc, SantaClara, Calif., USA (see for example data regarding the Human Genome U133(HG-U133) Set atwww.affymetrix.com/products/arrays/specific/hgu133.affx; GeneChip HumanGenome U133A 2.0 Array atwww.affymetrix.com/products/arrays/specific/hgu133av2.affx; and HumanGenome U133 Plus 2.0 Array atwww.affymetrix.com/products/arrays/specific/hgu133plus.affx). The probenames follow the Affymetrix naming convention. The data is availablefrom NCBI Gene Expression Omnibus (seewww.ncbi.nlm.nih.gov/projects/geo/ and Edgar et al, Nucleic AcidsResearch, 2002, Vol. 30, No. 1 207-210). The dataset (including results)is available from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1133 forthe Series GSE1133 database (published on March 2004); a reference tothese results is as follows: Su et al (Proc Natl Acad Sci USA. 2004 Apr.20; 101(16):6062-7. Epub 2004 Apr. 9).

Oligonucleotide microarray results taken from Affymetrix data were fromchips available from Affymetrix Inc, Santa Clara, Calif., USA (see forexample data regarding the Human Genome U133 (HG-U133) Set atwww.affymetrix.com/products/arrays/specific/hgu133.affx; GeneChip HumanGenome U133A 2.0 Array atwww.affymetrix.com/products/arrays/specific/hgu133av2.affx; and HumanGenome U133 Plus 2.0 Array atwww.affymetrix.com/products/arrays/specific/hgu133plus.affx). The probenames follow the Affymetrix naming convention. The data is availablefrom NCBI Gene Expression Omnibus (seewww.ncbi.nlm.nih.gov/projects/geo/ and Edgar et al, Nucleic AcidsResearch, 2002, Vol. 30, No. 1 207-210). The dataset (including results)is available from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1133 forthe Series GSE1133 database (published on March 2004); a reference tothese results is as follows: Su et al (Proc Natl Acad Sci USA. 2004 Apr.20; 101(16):6062-7. Epub 2004 Apr. 9).

The following list of abbreviations for tissues was used in the TAAhistograms. The term “TAA” stands for “Tumor Associated Antigen”, andthe TAA histograms, given in the text, represent the cancerous tissueexpression pattern as predicted by the biomarkers selection engine, asdescribed in detail in examples 1-5 below (the first word is theabbreviation while the second word is the full name):

(“BONE”, “bone”);(“COL”, “colon”);(“EPI”, “epithelial”);(“GEN”, “general”);(“LIVER”, “liver”);(“LUN”, “lung”);(“LYMPH”, “lymph nodes”);(“MARROW”, “bone marrow”);(“OVA”, “ovary”);(“PANCREAS”, “pancreas”);(“PRO”, “prostate”);(“STOMACH”, “stomach”);(“TCELL”, “T cells”);

(“THYROID”, “Thyroid”);

(“MAM”, “breast”);(“BRAIN”, “brain”);(“UTERUS”, “uterus”);(“SKIN”, “skin”);(“KIDNEY”, “kidney”);(“MUSCLE”, “muscle”);(“ADREN”, “adrenal”);(“HEAD”, “head and neck”);(“BLADDER”, “bladder”);

It should be noted that the terms “segment”, “seg” and “node”(abbreviated as “N” in the names of nodes) are used interchangeably inreference to nucleic acid sequences of the present invention, they referto portions of nucleic acid sequences that were shown to have one ormore properties as described herein. They are also the building blocksthat were used to construct complete nucleic acid sequences as describedin greater detail elsewhere herein. Optionally and preferably, they areexamples of oligonucleotides which are embodiments of the presentinvention, for example as amplicons, hybridization units and/or fromwhich primers and/or complementary oligonucleotides may optionally bederived, and/or for any other use.

In some embodiments, the phrase “disease” refers to its commonlyunderstood meaning, and includes, inter alia, any type of pathologyand/or damage, including both chronic and acute damage, as well as aprogress from acute to chronic damage.

In some embodiments, the phrase “marker” in the context of the presentinvention refers to a nucleic acid fragment, a peptide, or apolypeptide, which is differentially present in a sample taken frompatients (subjects) having one of the herein-described diseases orconditions, as compared to a comparable sample taken from subjects whodo not have one the above-described diseases or conditions.

In some embodiments, the phrase “differentially present” refers todifferences in the quantity or quality of a marker present in a sampletaken from patients having one of the herein-described diseases orconditions as compared to a comparable sample taken from patients who donot have one of the herein-described diseases or conditions. Forexample, a nucleic acid fragment may optionally be differentiallypresent between the two samples if the amount of the nucleic acidfragment in one sample is significantly different from the amount of thenucleic acid fragment in the other sample, for example as measured byhybridization and/or NAT-based assays. A polypeptide is differentiallypresent between the two samples if the amount of the polypeptide in onesample is significantly different from the amount of the polypeptide inthe other sample. It should be noted that if the marker is detectable inone sample and not detectable in the other, then such a marker can beconsidered to be differentially present. Optionally, a relatively lowamount of up-regulation may serve as the marker, as described herein.One of ordinary skill in the art could easily determine such relativelevels of the markers; further guidance is provided in the descriptionof each individual marker below.

In some embodiments, the phrase “diagnostic” means identifying thepresence or nature of a pathologic condition. Diagnostic methods differin their sensitivity and specificity. The “sensitivity” of a diagnosticassay is the percentage of diseased individuals who test positive(percent of “true positives”). Diseased individuals not detected by theassay are “false negatives.” Subjects who are not diseased and who testnegative in the assay are termed “true negatives.” The “specificity” ofa diagnostic assay is 1 minus the false positive rate, where the “falsepositive” rate is defined as the proportion of those without the diseasewho test positive. While a particular diagnostic method may not providea definitive diagnosis of a condition, it suffices if the methodprovides a positive indication that aids in diagnosis.

In some embodiments, the phrase “qualitative” when in reference todifferences in expression levels of a polynucleotide, polypeptide orcluster as described herein, refers to the presence versus absence ofexpression, or in some embodiments, the temporal regulation ofexpression, or in some embodiments, the timing of expression, or in someembodiments, the variant expressed, or in some embodiments, anypost-translational modifications to the expressed molecule, and others,as will be appreciated by one skilled in the art. In some embodiments,the phrase “quantitative” when in reference to differences in expressionlevels of a polynucleotide, polypeptide or cluster as described herein,refers to absolute differences in quantity of expression, as determinedby any means, known in the art, or in other embodiments, relativedifferences, which may be statistically significant, or in someembodiments, when viewed as a whole or over a prolonged period of time,etc., indicate a trend in terms of differences in expression.

In some embodiments, the term “diagnosing” refers to classifying adisease or a symptom, determining a severity of the disease, monitoringdisease progression, forecasting an outcome of a disease and/orprospects of recovery. The term “detecting” may also optionallyencompass any of the above.

Diagnosis of a disease according to the present invention can, in someembodiments, be effected by determining a level of a polynucleotide or apolypeptide of the present invention in a biological sample obtainedfrom the subject, wherein the level determined can be correlated withpredisposition to, or presence or absence of the disease. It should benoted that a “biological sample obtained from the subject” may alsooptionally comprise a sample that has not been physically removed fromthe subject, as described in greater detail below.

In some embodiments, the term “level” refers to expression levels of RNAand/or protein or to DNA copy number of a marker of the presentinvention.

Typically the level of the marker in a biological sample obtained fromthe subject is different (i.e., increased or decreased) from the levelof the same variant in a similar sample obtained from a healthyindividual (examples of biological samples are described herein).

Numerous well known tissue or fluid collection methods can be utilizedto collect the biological sample from the subject in order to determinethe level of DNA, RNA and/or polypeptide of the variant of interest inthe subject.

Examples include, but are not limited to, fine needle biopsy, needlebiopsy, core needle biopsy and surgical biopsy (e.g., brain biopsy), andlavage. Regardless of the procedure employed, once a biopsy/sample isobtained the level of the variant can be determined and a diagnosis canthus be made.

Determining the level of the same variant in normal tissues of the sameorigin is preferably effected along-side to detect an elevatedexpression and/or amplification and/or a decreased expression, of thevariant as opposed to the normal tissues.

In some embodiments, the term “test amount” of a marker refers to anamount of a marker in a subject's sample that is consistent with adiagnosis of a particular disease or condition. A test amount can beeither in absolute amount (e.g., microgram/ml) or a relative amount(e.g., relative intensity of signals).

In some embodiments, the term “control amount” of a marker can be anyamount or a range of amounts to be compared against a test amount of amarker. For example, a control amount of a marker can be the amount of amarker in a patient with a particular disease or condition or a personwithout such a disease or condition. A control amount can be either inabsolute amount (e.g., microgram/ml) or a relative amount (e.g.,relative intensity of signals).

In some embodiments, the term “detect” refers to identifying thepresence, absence or amount of the object to be detected.

In some embodiments, the term “label” includes any moiety or itemdetectable by spectroscopic, photo chemical, biochemical,immunochemical, or chemical means. For example, useful labels include³²P, ³⁵S, fluorescent dyes, electron-dense reagents, enzymes (e.g., ascommonly used in an ELISA), biotin-streptavadin, dioxigenin, haptens andproteins for which antisera or monoclonal antibodies are available, ornucleic acid molecules with a sequence complementary to a target. Thelabel often generates a measurable signal, such as a radioactive,chromogenic, or fluorescent signal, that can be used to quantify theamount of bound label in a sample. The label can be incorporated in orattached to a primer or probe either covalently, or through ionic, vander Waals or hydrogen bonds, e.g., incorporation of radioactivenucleotides, or biotinylated nucleotides that are recognized bystreptavadin. The label may be directly or indirectly detectable.Indirect detection can involve the binding of a second label to thefirst label, directly or indirectly. For example, the label can be theligand of a binding partner, such as biotin, which is a binding partnerfor streptavadin, or a nucleotide sequence, which is the binding partnerfor a complementary sequence, to which it can specifically hybridize.The binding partner may itself be directly detectable, for example, anantibody may be itself labeled with a fluorescent molecule. The bindingpartner also may be indirectly detectable, for example, a nucleic acidhaving a complementary nucleotide sequence can be a part of a branchedDNA molecule that is in turn detectable through hybridization with otherlabeled nucleic acid molecules (see, e.g., P. D. Fahrlander and A.Klausner, Bio/Technology 6:1165 (1988)). Quantitation of the signal isachieved by, e.g., scintillation counting, densitometry, or flowcytometry.

Exemplary detectable labels, optionally and preferably for use withimmunoassays, include but are not limited to magnetic beads, fluorescentdyes, radiolabels, enzymes (e.g., horse radish peroxide, alkalinephosphatase and others commonly used in an ELISA), and calorimetriclabels such as colloidal gold or colored glass or plastic beads.Alternatively, the marker in the sample can be detected using anindirect assay, wherein, for example, a second, labeled antibody is usedto detect bound marker-specific antibody, and/or in a competition orinhibition assay wherein, for example, a monoclonal antibody which bindsto a distinct epitope of the marker are incubated simultaneously withthe mixture.

“Immunoassay” is an assay that uses an antibody to specifically bind anantigen. The immunoassay is characterized by the use of specific bindingproperties of a particular antibody to isolate, target, and/or quantifythe antigen.

The phrase “specifically (or selectively) binds” to an antibody or“specifically (or selectively) immunoreactive with,” or “specificallyinteracts or binds” when referring to a protein or peptide (or otherepitope), refers, in some embodiments, to a binding reaction that isdeterminative of the presence of the protein in a heterogeneouspopulation of proteins and other biologics. Thus, under designatedimmunoassay conditions, the specified antibodies bind to a particularprotein at least two times greater than the background (non-specificsignal) and do not substantially bind in a significant amount to otherproteins present in the sample. Specific binding to an antibody undersuch conditions may require an antibody that is selected for itsspecificity for a particular protein. For example, polyclonal antibodiesraised to seminal basic protein from specific species such as rat,mouse, or human can be selected to obtain only those polyclonalantibodies that are specifically immunoreactive with seminal basicprotein and not with other proteins, except for polymorphic variants andalleles of seminal basic protein. This selection may be achieved bysubtracting out antibodies that cross-react with seminal basic proteinmolecules from other species. A variety of immunoassay formats may beused to select antibodies specifically immunoreactive with a particularprotein. For example, solid-phase ELISA immunoassays are routinely usedto select antibodies specifically immunoreactive with a protein (see,e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988), for adescription of immunoassay formats and conditions that can be used todetermine specific immunoreactivity). Typically a specific or selectivereaction will be at least twice background signal or noise and moretypically more than 10 to 100 times background.

In another embodiment, the present invention relates to bridges, tails,heads and/or insertions, and/or analogs, homologs and derivatives ofsuch peptides. Such bridges, tails, heads and/or insertions aredescribed in greater detail below with regard to the Examples.

In some embodiments, the term “tail” refers to a peptide sequence at theend of an amino acid sequence that is unique to a splice variantaccording to the present invention. Therefore, a splice variant havingsuch a tail may optionally be considered as a chimera, in that at leasta first portion of the splice variant is typically highly homologous(often 100% identical) to a portion of the corresponding known protein,while at least a second portion of the variant comprises the tail.

In some embodiments, the term “head” refers to a peptide sequence at thebeginning of an amino acid sequence that is unique to a splice variantaccording to the present invention. Therefore, a splice variant havingsuch a head may optionally be considered as a chimera, in that at leasta first portion of the splice variant comprises the head, while at leasta second portion is typically highly homologous (often 100% identical)to a portion of the corresponding known protein.

In some embodiments, the term “an edge portion” refers to a connectionbetween two portions of a splice variant according to the presentinvention that were not joined in the wild type or known protein. Anedge may optionally arise due to a join between the above “knownprotein” portion of a variant and the tail, for example, and/or mayoccur if an internal portion of the wild type sequence is no longerpresent, such that two portions of the sequence are now contiguous inthe splice variant that were not contiguous in the known protein. A“bridge” may optionally be an edge portion as described above, but mayalso include a join between a head and a “known protein” portion of avariant, or a join between a tail and a “known protein” portion of avariant, or a join between an insertion and a “known protein” portion ofa variant.

In some embodiments, a bridge between a tail or a head or a uniqueinsertion, and a “known protein” portion of a variant, comprises atleast about 10 amino acids, or in some embodiments at least about 20amino acids, or in some embodiments at least about 30 amino acids, or insome embodiments at least about 40 amino acids, in which at least oneamino acid is from the tail/head/insertion and at least one amino acidis from the “known protein” portion of a variant. In some embodiments,the bridge may comprise any number of amino acids from about 10 to about40 amino acids (for example, 10, 11, 12, 13.37, 38, 39, 40 amino acidsin length, or any number in between).

It should be noted that a bridge cannot be extended beyond the length ofthe sequence in either direction, and it should be assumed that everybridge description is to be read in such manner that the bridge lengthdoes not extend beyond the sequence itself.

Furthermore, bridges are described with regard to a sliding window incertain contexts below. For example, certain descriptions of the bridgesfeature the following format: a bridge between two edges (in which aportion of the known protein is not present in the variant) mayoptionally be described as follows: a bridge portion of CONTIG-NAME_P1(representing the name of the protein), comprising a polypeptide havinga length “n”, wherein n is at least about 10 amino acids in length,optionally at least about 20 amino acids in length, preferably at leastabout 30 amino acids in length, more preferably at least about 40 aminoacids in length and most preferably at least about 50 amino acids inlength, wherein at least two amino acids comprise XX (2 amino acids inthe center of the bridge, one from each end of the edge), having astructure as follows (numbering according to the sequence ofCONTIG-NAME_P1): a sequence starting from any of amino acid numbers 49−xto 49 (for example); and ending at any of amino acid numbers50+((n−2)−x) (for example), in which x varies from 0 to n−2. In thisexample, it should also be read as including bridges in which n is anynumber of amino acids between 10-50 amino acids in length. Furthermore,the bridge polypeptide cannot extend beyond the sequence, so it shouldbe read such that 49−x (for example) is not less than 1, nor50+((n−2)−x) (for example) greater than the total sequence length.

In another embodiment, this invention provides isolated nucleic acidmolecules, which in some embodiments encode for splice variants, havinga nucleotide sequence as set forth in any one of the sequences listedherein, being homologous to such sequences, at a percent as describedherein, or a sequence complementary thereto. In another embodiment, thisinvention provides an oligonucleotide of at least about 12 nucleotides,which specifically hybridizes with the nucleic acid molecules of thisinvention. In another embodiment, this invention provides vectors,cells, liposomes and compositions comprising the isolated nucleic acidsor polypeptides of this invention, as appropriate.

In another embodiment, this invention provides a method for detectingthe polypeptides of this invention in a biological sample, comprising:contacting a biological sample with an antibody specifically recognizinga splice variant according to the present invention under conditionswhereby the antibody specifically interacts with the splice variant inthe biological sample but do not recognize known corresponding proteins(wherein the known protein is discussed with regard to its splicevariant(s) in the Examples below), and detecting said interaction;wherein the presence of an interaction correlates with the presence of asplice variant in the biological sample.

In another embodiment, this invention provides a method for detecting apolynucleotide of this invention in a biological sample, comprising:hybridizing the isolated nucleic acid molecules or oligonucleotidefragments of at least about a minimum length to a nucleic acid materialof a biological sample and detecting a hybridization complex; whereinthe presence of a hybridization complex correlates with the presence ofa the polynucleotide in the biological sample.

In some embodiments of the present invention, thepolypeptides/polynucleotides described herein are non-limiting examplesof markers for diagnosing marker-detectable disease and/or an indicativecondition. Each polypeptide/polynucleotide marker of the presentinvention can be used alone or in combination, for various uses,including but not limited to, prognosis, prediction, screening, earlydiagnosis, determination of progression, therapy selection and treatmentmonitoring of marker-detectable disease and/or an indicative condition,including a transition from an indicative condition to marker-detectabledisease.

According to some embodiments of the present invention, any markeraccording to the present invention may optionally be used alone orcombination. Such a combination may optionally comprise a plurality ofmarkers described herein, optionally including any subcombination ofmarkers, and/or a combination featuring at least one other marker, forexample a known marker. Furthermore, such a combination may optionallyand preferably be used as described above with regard to determining aratio between a quantitative or semi-quantitative measurement of anymarker described herein to any other marker described herein, and/or anyother known marker, and/or any other marker. With regard to such a ratiobetween any marker described herein (or a combination thereof) and aknown marker, more preferably the known marker comprises the “knownprotein” as described in greater detail below with regard to eachcluster or gene.

In some embodiments of the present invention, there are provided ofmethods, uses, devices and assays for the diagnosis of a disease orcondition. Optionally a plurality of biomarkers (or markers) may be usedwith the present invention. The plurality of markers may optionallyinclude a plurality of markers described herein, and/or one or moreknown markers. The plurality of markers is preferably then correlatedwith the disease or condition. For example, such correlating mayoptionally comprise determining the concentration of each of theplurality of markers, and individually comparing each markerconcentration to a threshold level. Optionally, if the markerconcentration is above or below the threshold level (depending upon themarker and/or the diagnostic test being performed), the markerconcentration correlates with the disease or condition. Optionally andpreferably, a plurality of marker concentrations correlate with thedisease or condition.

Alternatively, such correlating may optionally comprise determining theconcentration of each of the plurality of markers, calculating a singleindex value based on the concentration of each of the plurality ofmarkers, and comparing the index value to a threshold level.

Also alternatively, such correlating may optionally comprise determininga temporal change in at least one of the markers, and wherein thetemporal change is used in the correlating step.

Also alternatively, such correlating may optionally comprise determiningwhether at least “X” number of the plurality of markers has aconcentration outside of a predetermined range and/or above or below athreshold (as described above). The value of “X” may optionally be onemarker, a plurality of markers or all of the markers; alternatively oradditionally, rather than including any marker in the count for “X”, oneor more specific markers of the plurality of markers may optionally berequired to correlate with the disease or condition (according to arange and/or threshold).

Also alternatively, such correlating may optionally comprise determiningwhether a ratio of marker concentrations for two markers is outside arange and/or above or below a threshold. Optionally, if the ratio isabove or below the threshold level and/or outside a range, the ratiocorrelates with the disease or condition.

Optionally, a combination of two or more these correlations may be usedwith a single panel and/or for correlating between a plurality ofpanels.

Optionally, the method distinguishes a disease or condition with asensitivity of at least 70% at a specificity of at least 85% whencompared to normal subjects. As used herein, sensitivity relates to thenumber of positive (diseased) samples detected out of the total numberof positive samples present; specificity relates to the number of truenegative (non-diseased) samples detected out of the total number ofnegative samples present. Preferably, the method distinguishes a diseaseor condition with a sensitivity of at least 80% at a specificity of atleast 90% when compared to normal subjects. More preferably, the methoddistinguishes a disease or condition with a sensitivity of at least 90%at a specificity of at least 90% when compared to normal subjects. Alsomore preferably, the method distinguishes a disease or condition with asensitivity of at least 70% at a specificity of at least 85% whencompared to subjects exhibiting symptoms that mimic disease or conditionsymptoms.

A marker panel may be analyzed in a number of fashions well known tothose of skill in the art. For example, each member of a panel may becompared to a “normal” value, or a value indicating a particularoutcome. A particular diagnosis/prognosis may depend upon the comparisonof each marker to this value; alternatively, if only a subset of markersare outside of a normal range, this subset may be indicative of aparticular diagnosis/prognosis. The skilled artisan will also understandthat diagnostic markers, differential diagnostic markers, prognosticmarkers, time of onset markers, disease or condition differentiatingmarkers, etc., may be combined in a single assay or device. Markers mayalso be commonly used for multiple purposes by, for example, applying adifferent threshold or a different weighting factor to the marker forthe different purpose(s).

In one embodiment, the panels comprise markers for the followingpurposes: diagnosis of a disease; diagnosis of disease and indication ifthe disease is in an acute phase and/or if an acute attack of thedisease has occurred; diagnosis of disease and indication if the diseaseis in a non-acute phase and/or if a non-acute attack of the disease hasoccurred; indication whether a combination of acute and non-acute phasesor attacks has occurred; diagnosis of a disease and prognosis of asubsequent adverse outcome; diagnosis of a disease and prognosis of asubsequent acute or non-acute phase or attack; disease progression (forexample for cancer, such progression may include for example occurrenceor recurrence of metastasis).

The above diagnoses may also optionally include differential diagnosisof the disease to distinguish it from other diseases, including thosediseases that may feature one or more similar or identical symptoms.

In certain embodiments, one or more diagnostic or prognostic indicatorsare correlated to a condition or disease by merely the presence orabsence of the indicator(s). In other embodiments, threshold level(s) ofa diagnostic or prognostic indicator(s) can be established, and thelevel of the indicator(s) in a patient sample can simply be compared tothe threshold level(s). The sensitivity and specificity of a diagnosticand/or prognostic test depends on more than just the analytical“quality” of the test—they also depend on the definition of whatconstitutes an abnormal result. In practice, Receiver OperatingCharacteristic curves, or “ROC” curves, are typically calculated byplotting the value of a variable versus its relative frequency in“normal” and “disease” populations, and/or by comparison of results froma subject before, during and/or after treatment. For any particularmarker, a distribution of marker levels for subjects with and without adisease will likely overlap. Under such conditions, a test does notabsolutely distinguish normal from disease with 100% accuracy, and thearea of overlap indicates where the test cannot distinguish normal fromdisease. A threshold is selected, above which (or below which, dependingon how a marker changes with the disease) the test is considered to beabnormal and below which the test is considered to be normal. The areaunder the ROC curve is a measure of the probability that the perceivedmeasurement will allow correct identification of a condition.

The horizontal axis of the ROC curve represents (1-specificity), whichincreases with the rate of false positives. The vertical axis of thecurve represents sensitivity, which increases with the rate of truepositives. Thus, for a particular cutoff selected, the value of(1-specificity) may be determined, and a corresponding sensitivity maybe obtained. The area under the ROC curve is a measure of theprobability that the measured marker level will allow correctidentification of a disease or condition. Thus, the area under the ROCcurve can be used to determine the effectiveness of the test.

ROC curves can be used even when test results don't necessarily give anaccurate number. As long as one can rank results, one can create an ROCcurve. For example, results of a test on “disease” samples might beranked according to degree (say 1=low, 2=normal, and 3=high). Thisranking can be correlated to results in the “normal” population, and aROC curve created. These methods are well known in the art (see forexample Hanley et al., Radiology 143: 29-36 (1982), incorporated byreference as if fully set forth herein).

One or more markers may lack diagnostic or prognostic value whenconsidered alone, but when used as part of a panel, such markers may beof great value in determining a particular diagnosis/prognosis. In someembodiments, particular thresholds for one or more markers in a panelare not relied upon to determine if a profile of marker levels obtainedfrom a subject are indicative of a particular diagnosis/prognosis.Rather, the present invention may utilize an evaluation of the entiremarker profile by plotting ROC curves for the sensitivity of aparticular panel of markers versus 1-(specificity) for the panel atvarious cutoffs. In these methods, a profile of marker measurements froma subject is considered together to provide a global probability(expressed either as a numeric score or as a percentage risk) that anindividual has had a disease, is at risk for developing such a disease,optionally the type of disease which the individual has had or is atrisk for, and so forth etc. In such embodiments, an increase in acertain subset of markers may be sufficient to indicate a particulardiagnosis/prognosis in one patient, while an increase in a differentsubset of markers may be sufficient to indicate the same or a differentdiagnosis/prognosis in another patient. Weighting factors may also beapplied to one or more markers in a panel, for example, when a marker isof particularly high utility in identifying a particulardiagnosis/prognosis, it may be weighted so that at a given level italone is sufficient to signal a positive result. Likewise, a weightingfactor may provide that no given level of a particular marker issufficient to signal a positive result, but only signals a result whenanother marker also contributes to the analysis.

In some embodiments, markers and/or marker panels are selected toexhibit at least 70% sensitivity, more preferably at least 80%sensitivity, even more preferably at least 85% sensitivity, still morepreferably at least 90% sensitivity, and most preferably at least 95%sensitivity, combined with at least 70% specificity, more preferably atleast 80% specificity, even more preferably at least 85% specificity,still more preferably at least 90% specificity, and most preferably atleast 95% specificity. In some embodiments, both the sensitivity andspecificity are at least 75%, more preferably at least 80%, even morepreferably at least 85%, still more preferably at least 90%, and mostpreferably at least 95%. Sensitivity and/or specificity may optionallybe determined as described above, with regard to the construction of ROCgraphs and so forth, for example.

According to some embodiments of the present invention, individualmarkers and/or combinations (panels) of markers may optionally be usedfor diagnosis of time of onset of a disease or condition. Such diagnosismay optionally be useful for a wide variety of conditions, preferablyincluding those conditions with an abrupt onset.

The phrase “determining the prognosis” as used herein refers to methodsby which the skilled artisan can predict the course or outcome of acondition in a patient. The term “prognosis” does not refer to theability to predict the course or outcome of a condition with 100%accuracy, or even that a given course or outcome is more likely to occurthan not. Instead, the skilled artisan will understand that the term“prognosis” refers to an increased probability that a certain course oroutcome will occur; that is, that a course or outcome is more likely tooccur in a patient exhibiting a given condition, when compared to thoseindividuals not exhibiting the condition. For example, in individualsnot exhibiting the condition, the chance of a given outcome may be about3%. In some embodiments, a prognosis is about a 5% chance of a givenoutcome, about a 7% chance, about a 10% chance, about a 12% chance,about a 15% chance, about a 20% chance, about a 25% chance, about a 30%chance, about a 40% chance, about a 50% chance, about a 60% chance,about a 75% chance, about a 90% chance, and about a 95% chance. The term“about” in this context refers to +/−1%.

The skilled artisan will understand that associating a prognosticindicator with a predisposition to an adverse outcome is a statisticalanalysis. For example, a marker level of greater than 80 pg/mL maysignal that a patient is more likely to suffer from an adverse outcomethan patients with a level less than or equal to 80 pg/mL, as determinedby a level of statistical significance. Additionally, a change in markerconcentration from baseline levels may be reflective of patientprognosis, and the degree of change in marker level may be related tothe severity of adverse events. Statistical significance is oftendetermined by comparing two or more populations, and determining aconfidence interval and/or a p value. See, e.g., Dowdy and Wearden,Statistics for Research, John Wiley & Sons, New York, 1983. In oneembodiment the confidence intervals of the invention are 90%, 95%,97.5%, 98%, 99%, 99.5%, 99.9% and 99.99%, while preferred p values are0.1, 0.05, 0.025, 0.02, 0.01, 0.005, 0.001, and 0.0001. Exemplarystatistical tests for associating a prognostic indicator with apredisposition to an adverse outcome are described hereinafter.

In other embodiments, a threshold degree of change in the level of aprognostic or diagnostic indicator can be established, and the degree ofchange in the level of the indicator in a patient sample can simply becompared to the threshold degree of change in the level. A preferredthreshold change in the level for markers of the invention is about 5%,about 10%, about 15%, about 20%, about 25%, about 30%, about 50%, about75%, about 100%, and about 150%. The term “about” in this context refersto +/−10%. In yet other embodiments, a “nomogram” can be established, bywhich a level of a prognostic or diagnostic indicator can be directlyrelated to an associated disposition towards a given outcome. Theskilled artisan is acquainted with the use of such nomograms to relatetwo numeric values with the understanding that the uncertainty in thismeasurement is the same as the uncertainty in the marker concentrationbecause individual sample measurements are referenced, not populationaverages.

Exemplary, non-limiting methods and systems for identification ofsuitable biomarkers for marker panels are now described. Methods andsystems for the identification of one or more markers for the diagnosis,and in particular for the differential diagnosis, of disease have beendescribed previously. Suitable methods for identifying markers usefulfor the diagnosis of disease states are described in detail in U.S.patent application no. 2004-0126767, entitled METHOD AND SYSTEM FORDISEASE DETECTION USING MARKER COMBINATIONS, filed Dec. 27, 2002, herebyincorporated by reference in its entirety as if fully set forth herein.One skilled in the art will also recognize that univariate analysis ofmarkers can be performed and the data from the univariate analyses ofmultiple markers can be combined to form panels of markers todifferentiate different disease conditions.

In developing a panel of markers useful in diagnosis, data for a numberof potential markers may be obtained from a group of subjects by testingfor the presence or level of certain markers. The group of subjects isdivided into two sets, and preferably the first set and the second seteach have an approximately equal number of subjects. The first setincludes subjects who have been confirmed as having a disease or, moregenerally, being in a first condition state. For example, this first setof patients may be those that have recently had a disease and/or aparticular type of the disease. The confirmation of this condition statemay be made through more rigorous and/or expensive testing, preferablyaccording to a previously defined diagnostic standard. Hereinafter,subjects in this first set will be referred to as “diseased”.

The second set of subjects are simply those who do not fall within thefirst set. Subjects in this second set may be “non-diseased;” that is,normal subjects. Alternatively, subjects in this second set may beselected to exhibit one symptom or a constellation of symptoms thatmimic those symptoms exhibited by the “diseased” subjects.

The data obtained from subjects in these sets includes levels of aplurality of markers. Preferably, data for the same set of markers isavailable for each patient. This set of markers may include allcandidate markers which may be suspected as being relevant to thedetection of a particular disease or condition. Actual known relevanceis not required. Embodiments of the methods and systems described hereinmay be used to determine which of the candidate markers are mostrelevant to the diagnosis of the disease or condition. The levels ofeach marker in the two sets of subjects may be distributed across abroad range, e.g., as a Gaussian distribution. However, no distributionfit is required.

As noted above, a marker often is incapable of definitively identifyinga patient as either diseased or non-diseased. For example, if a patientis measured as having a marker level that falls within the overlappingregion, the results of the test will be useless in diagnosing thepatient. An artificial cutoff may be used to distinguish between apositive and a negative test result for the detection of the disease orcondition. Regardless of where the cutoff is selected, the effectivenessof the single marker as a diagnosis tool is unaffected. Changing thecutoff merely trades off between the number of false positives and thenumber of false negatives resulting from the use of the single marker.The effectiveness of a test having such an overlap is often expressedusing a ROC (Receiver Operating Characteristic) curve as describedabove.

As discussed above, the measurement of the level of a single marker mayhave limited usefulness. The measurement of additional markers providesadditional information, but the difficulty lies in properly combiningthe levels of two potentially unrelated measurements. In the methods andsystems according to embodiments of the present invention, data relatingto levels of various markers for the sets of diseased and non-diseasedpatients may be used to develop a panel of markers to provide a usefulpanel response. The data may be provided in a database such as MicrosoftAccess, Oracle, other SQL databases or simply in a data file. Thedatabase or data file may contain, for example, a patient identifiersuch as a name or number, the levels of the various markers present, andwhether the patient is diseased or non-diseased.

Next, an artificial cutoff region may be initially selected for eachmarker. The location of the cutoff region may initially be selected atany point, but the selection may affect the optimization processdescribed below. In this regard, selection near a suspected optimallocation may facilitate faster convergence of the optimizer. In anembodiment method, the cutoff region is initially centered about thecenter of the overlap region of the two sets of patients. In oneembodiment, the cutoff region may simply be a cutoff point. In otherembodiments, the cutoff region may have a length of greater than zero.In this regard, the cutoff region may be defined by a center value and amagnitude of length. In practice, the initial selection of the limits ofthe cutoff region may be determined according to a pre-selectedpercentile of each set of subjects. For example, a point above which apre-selected percentile of diseased patients are measured may be used asthe right (upper) end of the cutoff range.

Each marker value for each patient may then be mapped to an indicator.The indicator is assigned one value below the cutoff region and anothervalue above the cutoff region. For example, if a marker generally has alower value for non-diseased patients and a higher value for diseasedpatients, a zero indicator will be assigned to a low value for aparticular marker, indicating a potentially low likelihood of a positivediagnosis. In other embodiments, the indicator may be calculated basedon a polynomial. The coefficients of the polynomial may be determinedbased on the distributions of the marker values among the diseased andnon-diseased subjects.

The relative importance of the various markers may be indicated by aweighting factor. The weighting factor may initially be assigned as acoefficient for each marker. As with the cutoff region, the initialselection of the weighting factor may be selected at any acceptablevalue, but the selection may affect the optimization process. In thisregard, selection near a suspected optimal location may facilitatefaster convergence of the optimizer. In an embodiment method, acceptableweighting coefficients may range between zero and one, and an initialweighting coefficient for each marker may be assigned as 0.5. In oneembodiment, the initial weighting coefficient for each marker may beassociated with the effectiveness of that marker by itself. For example,a ROC curve may be generated for the single marker, and the area underthe ROC curve may be used as the initial weighting coefficient for thatmarker.

Next, a panel response may be calculated for each subject in each of thetwo sets. The panel response is a function of the indicators to whicheach marker level is mapped and the weighting coefficients for eachmarker. One advantage of using an indicator value rather than the markervalue is that an extraordinarily high or low marker levels do not changethe probability of a diagnosis of diseased or non-diseased for thatparticular marker. Typically, a marker value above a certain levelgenerally indicates a certain condition state. Marker values above thatlevel indicate the condition state with the same certainty. Thus, anextraordinarily high marker value may not indicate an extraordinarilyhigh probability of that condition state. The use of an indicator whichis constant on one side of the cutoff region eliminates this concern.

The panel response may also be a general function of several parametersincluding the marker levels and other factors including, for example,race and gender of the patient. Other factors contributing to the panelresponse may include the slope of the value of a particular marker overtime. For example, a patient may be measured when first arriving at thehospital for a particular marker. The same marker may be measured againan hour later, and the level of change may be reflected in the panelresponse. Further, additional markers may be derived from other markersand may contribute to the value of the panel response. For example, theratio of values of two markers may be a factor in calculating the panelresponse.

Having obtained panel responses for each subject in each set ofsubjects, the distribution of the panel responses for each set may nowbe analyzed. An objective function may be defined to facilitate theselection of an effective panel. The objective function should generallybe indicative of the effectiveness of the panel, as may be expressed by,for example, overlap of the panel responses of the diseased set ofsubjects and the panel responses of the non-diseased set of subjects. Inthis manner, the objective function may be optimized to maximize theeffectiveness of the panel by, for example, minimizing the overlap.

In a some embodiment, the ROC curve representing the panel responses ofthe two sets of subjects may be used to define the objective function.For example, the objective function may reflect the area under the ROCcurve. By maximizing the area under the curve, one may maximize theeffectiveness of the panel of markers. In other embodiments, otherfeatures of the ROC curve may be used to define the objective function.For example, the point at which the slope of the ROC curve is equal toone may be a useful feature. In other embodiments, the point at whichthe product of sensitivity and specificity is a maximum, sometimesreferred to as the “knee,” may be used. In an embodiment, thesensitivity at the knee may be maximized. In further embodiments, thesensitivity at a predetermined specificity level may be used to definethe objective function. Other embodiments may use the specificity at apredetermined sensitivity level may be used. In still other embodiments,combinations of two or more of these ROC-curve features may be used.

It is possible that one of the markers in the panel is specific to thedisease or condition being diagnosed. When such markers are present atabove or below a certain threshold, the panel response may be set toreturn a “positive” test result. When the threshold is not satisfied,however, the levels of the marker may nevertheless be used as possiblecontributors to the objective function.

An optimization algorithm may be used to maximize or minimize theobjective function. Optimization algorithms are well-known to thoseskilled in the art and include several commonly available minimizing ormaximizing functions including the Simplex method and other constrainedoptimization techniques. It is understood by those skilled in the artthat some minimization functions are better than others at searching forglobal minimums, rather than local minimums. In the optimizationprocess, the location and size of the cutoff region for each marker maybe allowed to vary to provide at least two degrees of freedom permarker. Such variable parameters are referred to herein as independentvariables. In one embodiment, the weighting coefficient for each markeris also allowed to vary across iterations of the optimization algorithm.In various embodiments, any permutation of these parameters may be usedas independent variables.

In addition to the above-described parameters, the sense of each markermay also be used as an independent variable. For example, in many cases,it may not be known whether a higher level for a certain marker isgenerally indicative of a diseased state or a non-diseased state. Insuch a case, it may be useful to allow the optimization process tosearch on both sides. In practice, this may be implemented in severalways. For example, in one embodiment, the sense may be a truly separateindependent variable which may be flipped between positive and negativeby the optimization process. Alternatively, the sense may be implementedby allowing the weighting coefficient to be negative.

The optimization algorithm may be provided with certain constraints aswell. For example, the resulting ROC curve may be constrained to providean area-under-curve of greater than a particular value. ROC curveshaving an area under the curve of 0.5 indicate complete randomness,while an area under the curve of 1.0 reflects perfect separation of thetwo sets. Thus, a minimum acceptable value, such as 0.75, may be used asa constraint, particularly if the objective function does notincorporate the area under the curve. Other constraints may includelimitations on the weighting coefficients of particular markers.Additional constraints may limit the sum of all the weightingcoefficients to a particular value, such as 1.0.

The iterations of the optimization algorithm generally vary theindependent parameters to satisfy the constraints while minimizing ormaximizing the objective function. The number of iterations may belimited in the optimization process. Further, the optimization processmay be terminated when the difference in the objective function betweentwo consecutive iterations is below a predetermined threshold, therebyindicating that the optimization algorithm has reached a region of alocal minimum or a maximum.

Thus, the optimization process may provide a panel of markers includingweighting coefficients for each marker and cutoff regions for themapping of marker values to indicators. In order to develop lower-costpanels which require the measurement of fewer marker levels, certainmarkers may be eliminated from the panel. In this regard, the effectivecontribution of each marker in the panel may be determined to identifythe relative importance of the markers. In one embodiment, the weightingcoefficients resulting from the optimization process may be used todetermine the relative importance of each marker. The markers with thelowest coefficients may be eliminated.

Individual panel response values may also be used as markers in themethods described herein. For example, a panel may be constructed from aplurality of markers, and each marker of the panel may be described by afunction and a weighting factor to be applied to that marker (asdetermined by the methods described above). Each individual marker levelis determined for a sample to be tested, and that level is applied tothe predetermined function and weighting factor for that particularmarker to arrive at a sample value for that marker. The sample valuesfor each marker are added together to arrive at the panel response forthat particular sample to be tested. For a “diseased” and “non-diseased”group of patients, the resulting panel responses may be treated as ifthey were just levels of another disease marker.

Measures of test accuracy may be obtained as described in Fischer etal., Intensive Care Med. 29: 1043-51, 2003 (hereby incorporated byreference as if fully set forth herein), and used to determine theeffectiveness of a given marker or panel of markers. These measuresinclude sensitivity and specificity, predictive values, likelihoodratios, diagnostic odds ratios, and ROC curve areas. As discussed above,suitable tests may exhibit one or more of the following results on thesevarious measures: at least 75% sensitivity, combined with at least 75%specificity; ROC curve area of at least 0.7, more preferably at least0.8, even more preferably at least 0.9, and most preferably at least0.95; and/or a positive likelihood ratio (calculated assensitivity/(1−specificity)) of at least 5, more preferably at least 10,and most preferably at least 20, and a negative likelihood ratio(calculated as (1−sensitivity)/specificity) of less than or equal to0.3, more preferably less than or equal to 0.2, and most preferably lessthan or equal to 0.1.

According to embodiments of the present invention, a splice variantprotein or a fragment thereof, or a splice variant nucleic acid sequenceor a fragment thereof, may be featured as a biomarker for detectingmarker-detectable disease and/or an indicative condition, such that abiomarker may optionally comprise any of the above.

According to still other embodiments, the present invention optionallyand preferably encompasses any amino acid sequence or fragment thereofencoded by a nucleic acid sequence corresponding to a splice variantprotein as described herein. Any oligopeptide or peptide relating tosuch an amino acid sequence or fragment thereof may optionally also(additionally or alternatively) be used as a biomarker, including butnot limited to the unique amino acid sequences of these proteins thatare depicted as tails, heads, insertions, edges or bridges. The presentinvention also optionally encompasses antibodies capable of recognizing,and/or being elicited by, such oligopeptides or peptides.

The present invention also optionally and preferably encompasses anynucleic acid sequence or fragment thereof, or amino acid sequence orfragment thereof, corresponding to a splice variant of the presentinvention as described above, optionally for any application.

Non-limiting examples of methods or assays are described below.

The present invention also relates to kits based upon such diagnosticmethods or assays.

Nucleic Acid Sequences and Oligonucleotides

Various embodiments of the present invention encompass nucleic acidsequences described hereinabove; fragments thereof, sequenceshybridizable therewith, sequences homologous thereto, sequences encodingsimilar polypeptides with different codon usage, altered sequencescharacterized by mutations, such as deletion, insertion or substitutionof one or more nucleotides, either naturally occurring or artificiallyinduced, either randomly or in a targeted fashion.

The present invention encompasses nucleic acid sequences describedherein; fragments thereof, sequences hybridizable therewith, sequenceshomologous thereto [e.g., at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 95% or more say 100% identical to the nucleic acid sequences setforth below], sequences encoding similar polypeptides with differentcodon usage, altered sequences characterized by mutations, such asdeletion, insertion or substitution of one or more nucleotides, eithernaturally occurring or man induced, either randomly or in a targetedfashion. The present invention also encompasses homologous nucleic acidsequences (i.e., which form a part of a polynucleotide sequence of thepresent invention) which include sequence regions unique to thepolynucleotides of the present invention.

In cases where the polynucleotide sequences of the present inventionencode previously unidentified polypeptides, the present invention alsoencompasses novel polypeptides or portions thereof, which are encoded bythe isolated polynucleotide and respective nucleic acid fragmentsthereof described hereinabove.

A “nucleic acid fragment” or an “oligonucleotide” or a “polynucleotide”are used herein interchangeably to refer to a polymer of nucleic acids.A polynucleotide sequence of the present invention refers to a single ordouble stranded nucleic acid sequences which is isolated and provided inthe form of an RNA sequence, a complementary polynucleotide sequence(cDNA), a genomic polynucleotide sequence and/or a compositepolynucleotide sequences (e.g., a combination of the above).

As used herein the phrase “complementary polynucleotide sequence” refersto a sequence, which results from reverse transcription of messenger RNAusing a reverse transcriptase or any other RNA dependent DNA polymerase.Such a sequence can be subsequently amplified in vivo or in vitro usinga DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to asequence derived (isolated) from a chromosome and thus it represents acontiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers toa sequence, which is composed of genomic and cDNA sequences. A compositesequence can include some exonal sequences required to encode thepolypeptide of the present invention, as well as some intronic sequencesinterposing therebetween. The intronic sequences can be of any source,including of other genes, and typically will include conserved splicingsignal sequences. Such intronic sequences may further include cis actingexpression regulatory elements.

Some embodiments of the present invention encompass oligonucleotideprobes.

An example of an oligonucleotide probe which can be utilized by thepresent invention is a single stranded polynucleotide which includes asequence complementary to the unique sequence region of any variantaccording to the present invention, including but not limited to anucleotide sequence coding for an amino sequence of a bridge, tail, headand/or insertion according to the present invention, and/or theequivalent portions of any nucleotide sequence given herein (includingbut not limited to a nucleotide sequence of a node, segment or amplicondescribed herein).

Alternatively, an oligonucleotide probe of the present invention can bedesigned to hybridize with a nucleic acid sequence encompassed by any ofthe above nucleic acid sequences, particularly the portions specifiedabove, including but not limited to a nucleotide sequence coding for anamino sequence of a bridge, tail, head and/or insertion according to thepresent invention, and/or the equivalent portions of any nucleotidesequence given herein (including but not limited to a nucleotidesequence of a node, segment or amplicon described herein).

Oligonucleotides designed according to the teachings of the presentinvention can be generated according to any oligonucleotide synthesismethod known in the art such as enzymatic synthesis or solid phasesynthesis. Equipment and reagents for executing solid-phase synthesisare commercially available from, for example, Applied Biosystems. Anyother means for such synthesis may also be employed; the actualsynthesis of the oligonucleotides is well within the capabilities of oneskilled in the art and can be accomplished via established methodologiesas detailed in, for example, “Molecular Cloning: A laboratory Manual”Sambrook et al., (1989); “Current Protocols in Molecular Biology”Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “CurrentProtocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md.(1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley &Sons, New York (1988) and “Oligonucleotide Synthesis” Gait, M. J., ed.(1984) utilizing solid phase chemistry, e.g. cyanoethyl phosphoramiditefollowed by deprotection, desalting and purification by for example, anautomated trityl-on method or HPLC.

Oligonucleotides used according to this aspect of the present inventionare those having a length selected from a range of about 10 to about 200bases preferably about 15 to about 150 bases, more preferably about 20to about 100 bases, most preferably about 20 to about 50 bases.Preferably, the oligonucleotide of the present invention features atleast 17, at least 18, at least 19, at least 20, at least 22, at least25, at least 30 or at least 40, bases specifically hybridizable with thebiomarkers of the present invention.

The oligonucleotides of the present invention may comprise heterocylicnucleosides consisting of purines and the pyrimidines bases, bonded in a3′ to 5′ phosphodiester linkage.

Preferably used oligonucleotides are those modified at one or more ofthe backbone, internucleoside linkages or bases, as is broadly describedhereinunder.

Specific examples of oligonucleotides useful according to this aspect ofthe present invention include oligonucleotides containing modifiedbackbones or non-natural internucleoside linkages. Oligonucleotideshaving modified backbones include those that retain a phosphorus atom inthe backbone, as disclosed in U.S. Pat. Nos. 4,469,863; 4,476,301;5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302;5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233;5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111;5,563,253; 5,571,799; 5,587,361; and 5,625,050.

Modified oligonucleotide backbones include, for example,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkyl phosphotriesters, methyl and other alkylphosphonates including 3′-alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Varioussalts, mixed salts and free acid forms can also be used.

Alternatively, modified oligonucleotide backbones that do not include aphosphorus atom therein have backbones that are formed by short chainalkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkylor cycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These includethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH₂ component parts, as disclosed in U.S. Pat. Nos. 5,034,506;5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562;5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677;5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240;5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360;5,677,437; and 5,677,439.

Other oligonucleotides which can be used according to the presentinvention, are those modified in both sugar and the internucleosidelinkage, i.e., the backbone, of the nucleotide units are replaced withnovel groups. The base units are maintained for complementation with theappropriate polynucleotide target. An example for such anoligonucleotide mimetic, includes peptide nucleic acid (PNA). UnitedStates patents that teach the preparation of PNA compounds include, butare not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262,each of which is herein incorporated by reference. Other backbonemodifications, which can be used in the present invention are disclosedin U.S. Pat. No. 6,303,374.

Oligonucleotides of the present invention may also include basemodifications or substitutions. As used herein, “unmodified” or“natural” bases include the purine bases adenine (A) and guanine (G),and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).Modified bases include but are not limited to other synthetic andnatural bases such as 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and otheralkyl derivatives of adenine and guanine, 2-propyl and other alkylderivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil andcytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil),4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl andother 8-substituted adenines and guanines, 5-halo particularly 5-bromo,5-trifluoromethyl and other 5-substituted uracils and cytosines,7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine,7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.Further bases particularly useful for increasing the binding affinity ofthe oligomeric compounds of the invention include 5-substitutedpyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines,including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.5-methylcytosine substitutions have been shown to increase nucleic acidduplex stability by 0.6-1.2° C. and are presently preferred basesubstitutions, even more particularly when combined with2′-O-methoxyethyl sugar modifications.

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates, which enhance the activity, cellular distribution orcellular uptake of the oligonucleotide. Such moieties include but arenot limited to lipid moieties such as a cholesterol moiety, cholic acid,a thioether, e.g., hexyl-5-tritylthiol, a thiocholesterol, an aliphaticchain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid, a palmityl moiety,or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety, asdisclosed in U.S. Pat. No. 6,303,374.

It is not necessary for all positions in a given oligonucleotidemolecule to be uniformly modified, and in fact more than one of theaforementioned modifications may be incorporated in a single compound oreven at a single nucleoside within an oligonucleotide.

It will be appreciated that oligonucleotides of the present inventionmay include further modifications for more efficient use as diagnosticagents and/or to increase bioavailability, therapeutic efficacy andreduce cytotoxicity.

To enable cellular expression of the polynucleotides of the presentinvention, a nucleic acid construct according to the present inventionmay be used, which includes at least a coding region of one of the abovenucleic acid sequences, and further includes at least one cis actingregulatory element. As used herein, the phrase “cis acting regulatoryelement” refers to a polynucleotide sequence, preferably a promoter,which binds a trans acting regulator and regulates the transcription ofa coding sequence located downstream thereto.

Any suitable promoter sequence can be used by the nucleic acid constructof the present invention.

In some embodiments, the promoter utilized by the nucleic acid constructof the present invention is active in the specific cell populationtransformed. Examples of cell type-specific and/or tissue-specificpromoters include promoters such as albumin that is liver specific,lymphoid specific promoters [Calame et al., (1988) Adv. Immunol.43:235-275]; in particular promoters of T-cell receptors [Winoto et al.,(1989) EMBO J. 8:729-733] and immunoglobulins; [Banerji et al. (1983)Cell 33729-740], neuron-specific promoters such as the neurofilamentpromoter [Byrne et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477],pancreas-specific promoters [Edlunch et al. (1985) Science 230:912-916]or mammary gland-specific promoters such as the milk whey promoter (U.S.Pat. No. 4,873,316 and European Application Publication No. 264,166).The nucleic acid construct of the present invention can further includean enhancer, which can be adjacent or distant to the promoter sequenceand can function in up regulating the transcription therefrom.

The nucleic acid construct of the present invention further includes, insome embodiments, an appropriate selectable marker and/or an origin ofreplication. In some embodiments, the nucleic acid construct utilized isa shuttle vector, which can propagate both in E. coli (wherein theconstruct comprises an appropriate selectable marker and origin ofreplication) and be compatible for propagation in cells, or integrationin a gene and a tissue of choice. The construct according to the presentinvention can be, for example, a plasmid, a bacmid, a phagemid, acosmid, a phage, a virus or an artificial chromosome.

In some embodiments, in vivo nucleic acid transfer techniques includetransfection with viral or non-viral constructs, such as adenovirus,lentivirus, retrovirus, Herpes simplex I virus, or adeno-associatedvirus (AAV) and lipid-based systems. Useful lipids for lipid-mediatedtransfer of the gene are, for example, DOTMA, DOPE, and DC-Chol[Tonkinson et al., Cancer Investigation, 14(1): 54-65 (1996)]. Suchvector constructs may comprise a packaging signal, long terminal repeats(LTRs) or portions thereof, and positive and negative strand primerbinding sites appropriate to the virus used. In addition, such aconstruct may include a signal sequence for secretion of the peptidefrom a host cell in which it is placed. Preferably the signal sequencefor this purpose is a mammalian signal sequence or the signal sequenceof the polypeptide variants of the present invention. Optionally, theconstruct may also include a signal that directs polyadenylation, aswell as one or more restriction sites and a translation terminationsequence. By way of example, such constructs may include a 5′ LTR, atRNA binding site, a packaging signal, an origin of second-strand DNAsynthesis, and a 3′ LTR or a portion thereof. Other vectors can be usedthat are non-viral, such as cationic lipids, polylysine, and dendrimers.

Variant Recombinant Expression Vectors and Host Cells

Another aspect of the invention pertains to vectors, preferablyexpression vectors, containing a nucleic acid encoding a variantprotein, or derivatives, fragments, analogs or homologs thereof. As usedherein, the term “vector” refers to a nucleic acid molecule capable oftransporting another nucleic acid to which it has been linked. One typeof vector is a “plasmid”, which refers to a circular double stranded DNAloop into which additional DNA segments can be ligated. Another type ofvector is a viral vector, wherein additional DNA segments can be ligatedinto the viral genome. Certain vectors are capable of autonomousreplication in a host cell into which they are introduced (e.g.,bacterial vectors having a bacterial origin of replication and episomalmammalian vectors). Other vectors (e.g., non-episomal mammalian vectors)are integrated into the genome of a host cell upon introduction into thehost cell, and thereby are replicated along with the host genome.Moreover, certain vectors are capable of directing the expression ofgenes to which they are operatively-linked. Such vectors are referred toherein as “expression vectors”. In general, expression vectors ofutility in recombinant DNA techniques are often in the form of plasmids.In the present specification, “plasmid” and “vector” can be usedinterchangeably as the plasmid is the most commonly used form of vector.However, the invention is intended to include such other forms ofexpression vectors, such as viral vectors (e.g., replication defectiveretroviruses, adenoviruses and adeno-associated viruses), which serveequivalent functions.

The recombinant expression vectors of the invention comprise a nucleicacid of the invention in a form suitable for expression of the nucleicacid in a host cell, which means that the recombinant expression vectorsinclude one or more regulatory sequences, selected on the basis of thehost cells to be used for expression, that is operatively-linked to thenucleic acid sequence to be expressed. Within a recombinant expressionvector, “operably-linked” is intended to mean that the nucleotidesequence of interest is linked to the regulatory sequence(s) in a mannerthat allows for expression of the nucleotide sequence (e.g., in an invitro transcription/translation system or in a host cell when the vectoris introduced into the host cell).

The term “regulatory sequence” is intended to include promoters,enhancers and other expression control elements (e.g., polyadenylationsignals). Such regulatory sequences are described, for example, inGoeddel, Gene Expression Technology Methods in Enzymology 185, AcademicPress, San Diego, Calif. (1990). Regulatory sequences include those thatdirect constitutive expression of a nucleotide sequence in many types ofhost cell and those that direct expression of the nucleotide sequenceonly in certain host cells (e.g., tissue-specific regulatory sequences).It will be appreciated by those skilled in the art that the design ofthe expression vector can depend on such factors as the choice of thehost cell to be transformed, the level of expression of protein desired,etc. The expression vectors of the invention can be introduced into hostcells to thereby produce proteins or peptides, including fusion proteinsor peptides, encoded by nucleic acids as described herein (e.g., variantproteins, mutant forms of variant proteins, fusion proteins, etc.).

The recombinant expression vectors of the invention can be designed forproduction of variant proteins in prokaryotic or eukaryotic cells. Forexample, variant proteins can be expressed in bacterial cells such asEscherichia coli, insect cells (using baculovirus expression vectors)yeast cells or mammalian cells. Suitable host cells are discussedfurther in Goeddel, Gene Expression Technology: Methods in Enzymology185, Academic Press, San Diego, Calif. (1990). Alternatively, therecombinant expression vector can be transcribed and translated invitro, for example using T7 promoter regulatory sequences and T7polymerase.

Expression of proteins in prokaryotes is most often carried out inEscherichia coli with vectors containing constitutive or induciblepromoters directing the expression of either fusion or non-fusionproteins. Fusion vectors add a number of amino acids to a proteinencoded therein, to the amino or carboxyl terminus of the recombinantprotein. Such fusion vectors typically serve three purposes: (i) toincrease expression of recombinant protein; (ii) to increase thesolubility of the recombinant protein; and (iii) to aid in thepurification of the recombinant protein by acting as a ligand inaffinity purification. Often, in fusion expression vectors, aproteolytic cleavage site is introduced at the junction of the fusionmoiety and the recombinant protein to enable separation of therecombinant protein from the fusion moiety subsequent to purification ofthe fusion protein. Such enzymes, and their cognate recognitionsequences, include Factor Xa, thrombin, PreScission, TEV andenterokinase. Typical fusion expression vectors include pGEX (PharmaciaBiotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New EnglandBiolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) andpTrcHis (Invitrogen Life Technologies) that fuse glutathioneS-transferase (GST), maltose E binding protein, protein A or 6×His,respectively, to the target recombinant protein.

Examples of suitable inducible non-fusion E. coli expression vectorsinclude pTrc (Amrann et al., (1988) Gene 69:301-315).

One strategy to maximize recombinant protein expression in E. coli is toexpress the protein in a host bacteria with an impaired capacity toproteolytically cleave the recombinant protein. See, e.g., Gottesman,Gene Expression Technology: Methods in Enzymology 185, Academic Press,San Diego, Calif. (1990) 119-128. Another strategy is to alter thenucleic acid sequence of the nucleic acid to be inserted into anexpression vector so that the individual codons for each amino acid arethose preferentially utilized in E. coli (see, e.g., Wada, et al., 1992.Nucl. Acids Res. 20: 2111-2118). Such alteration of nucleic acidsequences of the invention can be carried out by standard DNA synthesistechniques. Another optional strategy to solve codon bias is by usingBL21-codon plus bacterial strains (Invitrogen) or Rosetta bacterialstrain (Novagen), as these strains contain extra copies of rare E. colitRNA genes.

In another embodiment, the expression vector encoding for the variantprotein is a yeast expression vector. Examples of vectors for expressionin yeast Saccharomyces cerivisae include pYepSec1 (Baldari, et al.,1987. EMBO J. 6: 229-234), pMFa (Kurjan and Herskowitz, 1982. Cell 30:933-943), pJRY88 (Schultz et al., 1987. Gene 54: 113-123), pYES2(Invitrogen Corporation, San Diego, Calif.), and picZ (InVitrogen Corp,San Diego, Calif.).

Alternatively, variant protein can be produced in insect cells usingbaculovirus expression vectors. Baculovirus vectors available forexpression of proteins in cultured insect cells (e.g., SF9 cells)include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3:2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170:31-39).

In yet another embodiment, a nucleic acid of the invention is expressedin mammalian cells using a mammalian expression vector. Examples ofmammalian expression vectors include pCDM8 (Seed, 1987. Nature 329: 840)and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195), pIRESpuro(Clontech), pUB6 (Invitrogen), pCEP4 (Invitrogen) pREP4 (Invitrogen),pcDNA3 (Invitrogen). When used in mammalian cells, the expressionvector's control functions are often provided by viral regulatoryelements. For example, commonly used promoters are derived from polyoma,adenovirus 2, cytomegalovirus, Rous Sarcoma Virus, and simian virus 40.For other suitable expression systems for both prokaryotic andeukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al.,Molecular Cloning: A Laboratory Manual. 2nd ed., Cold Spring HarborLaboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989.

In another embodiment, the recombinant mammalian expression vector iscapable of directing expression of the nucleic acid preferentially in aparticular cell type (e.g., tissue-specific regulatory elements are usedto express the nucleic acid). Tissue-specific regulatory elements areknown in the art. Non-limiting examples of suitable tissue-specificpromoters include the albumin promoter (liver-specific; Pinkert, et al.,1987. Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame andEaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of Tcell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) andimmunoglobulins (Banerji, et al., 1983. Cell 33: 729-740; Queen andBaltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., theneurofilament promoter; Byrne and Ruddle, 1989. Proc. Natl. Acad. Sci.USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985.Science 230: 912-916), and mammary gland-specific promoters (e.g., milkwhey promoter; U.S. Pat. No. 4,873,316 and European ApplicationPublication No. 264,166). Developmentally-regulated promoters are alsoencompassed, e.g., the murine hox promoters (Kessel and Gruss, 1990.Science 249: 374-379) and the O-fetoprotein promoter (Campes andTilghman, 1989. Genes Dev. 3: 537-546).

The invention further provides a recombinant expression vectorcomprising a DNA molecule of the invention cloned into the expressionvector in an antisense orientation. That is, the DNA molecule isoperatively-linked to a regulatory sequence in a manner that allows forexpression (by transcription of the DNA molecule) of an RNA moleculethat is antisense to mRNA encoding for variant protein. Regulatorysequences operatively linked to a nucleic acid cloned in the antisenseorientation can be chosen that direct the continuous expression of theantisense RNA molecule in a variety of cell types, for instance viralpromoters and/or enhancers, or regulatory sequences can be chosen thatdirect constitutive, tissue specific or cell type specific expression ofantisense RNA. The antisense expression vector can be in the form of arecombinant plasmid, phagemid or attenuated virus in which antisensenucleic acids are produced under the control of a high efficiencyregulatory region, the activity of which can be determined by the celltype into which the vector is introduced. For a discussion of theregulation of gene expression using antisense genes see, e.g.,Weintraub, et al., “Antisense RNA as a molecular tool for geneticanalysis,” Reviews-Trends in Genetics, Vol. 1(1) 1986.

Another aspect of the invention pertains to host cells into which arecombinant expression vector of the invention has been introduced. Theterms “host cell” and “recombinant host cell” are used interchangeablyherein. It is understood that such terms refer not only to theparticular subject cell but also to the progeny or potential progeny ofsuch a cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

A host cell can be any prokaryotic or eukaryotic cell. For example,variant protein can be produced in bacterial cells such as E. coli,insect cells, yeast or mammalian cells (such as Chinese hamster ovarycells (CHO) or COS or 293 cells). Other suitable host cells are known tothose skilled in the art.

Vector DNA can be introduced into prokaryotic or eukaryotic cells viaconventional transformation or transfection techniques. As used herein,the terms “transformation” and “transfection” are intended to refer to avariety of art-recognized techniques for introducing foreign nucleicacid (e.g., DNA) into a host cell, including calcium phosphate orcalcium chloride co-precipitation, DEAE-dextran-mediated transfection,lipofection, or electroporation. Suitable methods for transforming ortransfecting host cells can be found in Sambrook, et al. (MolecularCloning: A Laboratory Manual. 2nd ed., Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989),and other laboratory manuals.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign DNA into their genome. Inorder to identify and select these integrants, a gene that encodes aselectable marker (e.g., resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest. Variousselectable markers include those that confer resistance to drugs, suchas G418, hygromycin, puromycin, blasticidin and methotrexate. Nucleicacids encoding a selectable marker can be introduced into a host cell onthe same vector as that encoding variant protein or can be introduced ona separate vector. Cells stably transfected with the introduced nucleicacid can be identified by drug selection (e.g., cells that haveincorporated the selectable marker gene will survive, while the othercells die).

A host cell of the invention, such as a prokaryotic or eukaryotic hostcell in culture, can be used to produce (i.e., express) variant protein.Accordingly, the invention further provides methods for producingvariant protein using the host cells of the invention. In oneembodiment, the method comprises culturing the host cell of the presentinvention (into which a recombinant expression vector encoding variantprotein has been introduced) in a suitable medium such that variantprotein is produced. In another embodiment, the method further comprisesisolating variant protein from the medium or the host cell.

For efficient production of the protein, it is preferable to place thenucleotide sequences encoding the variant protein under the control ofexpression control sequences optimized for expression in a desired host.For example, the sequences may include optimized transcriptional and/ortranslational regulatory sequences (such as altered Kozak sequences).

Hybridization Assays

Detection of a nucleic acid of interest in a biological sample mayoptionally be effected by hybridization-based assays using anoligonucleotide probe (non-limiting examples of probes according to thepresent invention were previously described).

Traditional hybridization assays include PCR, RT-PCR, Real-time PCR,RNase protection, in-situ hybridization, primer extension, Southernblots (DNA detection), dot or slot blots (DNA, RNA), and Northern blots(RNA detection) (NAT type assays are described in greater detail below).More recently, PNAs have been described (Nielsen et al. 1999, CurrentOpin. Biotechnol. 10:71-75). Other detection methods include kitscontaining probes on a dipstick setup and the like.

Hybridization based assays which allow the detection of a variant ofinterest (i.e., DNA or RNA) in a biological sample rely on the use ofoligonucleotides which can be 10, 15, 20, or 30 to 100 nucleotides longpreferably from 10 to 50, more preferably from 40 to 50 nucleotideslong.

Thus, the isolated polynucleotides (oligonucleotides) of the presentinvention are preferably hybridizable with any of the herein describednucleic acid sequences under moderate to stringent hybridizationconditions.

Moderate to stringent hybridization conditions are characterized by ahybridization solution such as containing 10% dextrane sulfate, 1 MNaCl, 1% SDS and 5×10⁶ cpm ³²P labeled probe, at 65° C., with a finalwash solution of 0.2×SSC and 0.1% SDS and final wash at 65° C. andwhereas moderate hybridization is effected using a hybridizationsolution containing 10% dextrane sulfate, 1 M NaCl, 1% SDS and 5×10⁶ cpm³²P labeled probe, at 65° C., with a final wash solution of 1×SSC and0.1% SDS and final wash at 50° C.

More generally, hybridization of short nucleic acids (below 200 bp inlength, e.g. 17-40 bp in length) can be effected using the followingexemplary hybridization protocols which can be modified according to thedesired stringency; (i) hybridization solution of 6×SSC and 1% SDS or 3M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5% SDS,100 μg/ml denatured salmon sperm DNA and 0.1% nonfat dried milk,hybridization temperature of 1-1.5° C. below the T_(m), final washsolution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH7.6), 0.5% SDS at 1-1.5° C. below the T_(m); (ii) hybridization solutionof 6×SSC and 0.1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1mM EDTA (pH 7.6), 0.5% SDS, 100 μg/ml denatured salmon sperm DNA and0.1% nonfat dried milk, hybridization temperature of 2-2.5° C. below theT_(m), final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH6.8), 1 mM EDTA (pH 7.6), 0.5% SDS at 1-1.5° C. below the T_(m), finalwash solution of 6×SSC, and final wash at 22° C.; (iii) hybridizationsolution of 6×SSC and 1% SDS or 3 M TMACI, 0.01 M sodium phosphate (pH6.8), 1 mM EDTA (pH 7.6), 0.5% SDS, 100 μg/ml denatured salmon sperm DNAand 0.1% nonfat dried milk, hybridization temperature.

The detection of hybrid duplexes can be carried out by a number ofmethods. Typically, hybridization duplexes are separated fromunhybridized nucleic acids and the labels bound to the duplexes are thendetected. Such labels refer to radioactive, fluorescent, biological orenzymatic tags or labels of standard use in the art. A label can beconjugated to either the oligonucleotide probes or the nucleic acidsderived from the biological sample.

Probes can be labeled according to numerous well known methods.Non-limiting examples of radioactive labels include 3H, 14C, 32P, and35S, Non-limiting examples of detectable markers include ligands,fluorophores, chemiluminescent agents, enzymes, and antibodies. Otherdetectable markers for use with probes, which can enable an increase insensitivity of the method of the invention, include biotin andradio-nucleotides. It will become evident to the person of ordinaryskill that the choice of a particular label dictates the manner in whichit is bound to the probe.

For example, oligonucleotides of the present invention can be labeledsubsequent to synthesis, by incorporating biotinylated dNTPs or rNTP, orsome similar means (e.g., photo-cross-linking a psoralen derivative ofbiotin to RNAs), followed by addition of labeled streptavidin (e.g.,phycoerythrin-conjugated streptavidin) or the equivalent, Alternatively,when fluorescently-labeled oligonucleotide probes are used, fluorescein,lissamine, phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3,Cy3.5, Cy5, Cy5.5, Cy7, Fluor X (Amersham) and others [e.g., Kricka etal. (1992), Academic Press San Diego, Calif.] can be attached to theoligonucleotides.

Those skilled in the art will appreciate that wash steps may be employedto wash away excess target DNA or probe as well as unbound conjugate.Further, standard heterogeneous assay formats are suitable for detectingthe hybrids using the labels present on the oligonucleotide primers andprobes.

It will be appreciated that a variety of controls may be usefullyemployed to improve accuracy of hybridization assays. For instance,samples may be hybridized to an irrelevant probe and treated with RNAseA prior to hybridization, to assess false hybridization.

Although the present invention is not specifically dependent on the useof a label for the detection of a particular nucleic acid sequence, sucha label might be beneficial, by increasing the sensitivity of thedetection. Furthermore, it enables automation. Probes can be labeledaccording to numerous well known methods.

As commonly known, radioactive nucleotides can be incorporated intoprobes of the invention by several methods. Non-limiting examples ofradioactive labels include 3H, 14C, 32P, and 35S.

Those skilled in the art will appreciate that wash steps may be employedto wash away excess target DNA or probe as well as unbound conjugate.Further, standard heterogeneous assay formats are suitable for detectingthe hybrids using the labels present on the oligonucleotide primers andprobes.

It will be appreciated that a variety of controls may be usefullyemployed to improve accuracy of hybridization assays.

Probes of the invention can be utilized with naturally occurringsugar-phosphate backbones as well as modified backbones includingphosphorothioates, dithionates, alkyl phosphonates and a-nucleotides andthe like. Probes of the invention can be constructed of eitherribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and preferably ofDNA.

NAT Assays

Detection of a nucleic acid of interest in a biological sample may alsooptionally be effected by NAT-based assays, which involve nucleic acidamplification technology, such as PCR for example (or variations thereofsuch as real-time PCR for example).

As used herein, a “primer” defines an oligonucleotide which is capableof annealing to (hybridizing with) a target sequence, thereby creating adouble stranded region which can serve as an initiation point for DNAsynthesis under suitable conditions.

Amplification of a selected, or target, nucleic acid sequence may becarried out by a number of suitable methods. See generally Kwoh et al.,1990, Am. Biotechnol. Lab. 8:14 Numerous amplification techniques havebeen described and can be readily adapted to suit particular needs of aperson of ordinary skill. Non-limiting examples of amplificationtechniques include polymerase chain reaction (PCR), ligase chainreaction (LCR), strand displacement amplification (SDA),transcription-based amplification, the q3 replicase system and NASBA(Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86, 1173-1177; Lizardi etal., 1988, BioTechnology 6:1197-1202; Malek et al., 1994, Methods Mol.Biol., 28:253-260; and Sambrook et al., 1989, supra).

The terminology “amplification pair” (or “primer pair”) refers herein toa pair of oligonucleotides (oligos) of the present invention, which areselected to be used together in amplifying a selected nucleic acidsequence by one of a number of types of amplification processes,preferably a polymerase chain reaction. Other types of amplificationprocesses include ligase chain reaction, strand displacementamplification, or nucleic acid sequence-based amplification, asexplained in greater detail below. As commonly known in the art, theoligos are designed to bind to a complementary sequence under selectedconditions.

In one particular embodiment, amplification of a nucleic acid samplefrom a patient is amplified under conditions which favor theamplification of the most abundant differentially expressed nucleicacid. In one embodiment, RT-PCR is carried out on an mRNA sample from apatient under conditions which favor the amplification of the mostabundant mRNA. In another embodiment, the amplification of thedifferentially expressed nucleic acids is carried out simultaneously. Itwill be realized by a person skilled in the art that such methods couldbe adapted for the detection of differentially expressed proteinsinstead of differentially expressed nucleic acid sequences.

The nucleic acid (i.e. DNA or RNA) for practicing the present inventionmay be obtained according to well known methods.

Oligonucleotide primers of the present invention may be of any suitablelength, depending on the particular assay format and the particularneeds and targeted genomes employed. Optionally, the oligonucleotideprimers are at least 12 nucleotides in length, preferably between 15 and24 molecules, and they may be adapted to be especially suited to achosen nucleic acid amplification system. As commonly known in the art,the oligonucleotide primers can be designed by taking into considerationthe melting point of hybridization thereof with its targeted sequence(Sambrook et al., 1989, Molecular Cloning—A Laboratory Manual, 2ndEdition, CSH Laboratories; Ausubel et al., 1989, in Current Protocols inMolecular Biology, John Wiley & Sons Inc., N.Y.).

It will be appreciated that antisense oligonucleotides may be employedto quantify expression of a splice isoform of interest. Such detectionis effected at the pre-mRNA level. Essentially the ability to quantitatetranscription from a splice site of interest can be effected based onsplice site accessibility. Oligonucleotides may compete with splicingfactors for the splice site sequences. Thus, low activity of theantisense oligonucleotide is indicative of splicing activity.

The polymerase chain reaction and other nucleic acid amplificationreactions are well known in the art (various non-limiting examples ofthese reactions are described in greater detail below). The pair ofoligonucleotides according to this aspect of the present invention arepreferably selected to have compatible melting temperatures (Tm), e.g.,melting temperatures which differ by less than that 7° C., preferablyless than 5° C., more preferably less than 4° C., most preferably lessthan 3° C., ideally between 3° C. and 0° C.

Polymerase Chain Reaction (PCR): The polymerase chain reaction (PCR), asdescribed in U.S. Pat. Nos. 4,683,195 and 4,683,202 to Mullis and Mulliset al., is a method of increasing the concentration of a segment oftarget sequence in a mixture of genomic DNA without cloning orpurification. This technology provides one approach to the problems oflow target sequence concentration. PCR can be used to directly increasethe concentration of the target to an easily detectable level. Thisprocess for amplifying the target sequence involves the introduction ofa molar excess of two oligonucleotide primers which are complementary totheir respective strands of the double-stranded target sequence to theDNA mixture containing the desired target sequence. The mixture isdenatured and then allowed to hybridize. Following hybridization, theprimers are extended with polymerase so as to form complementarystrands. The steps of denaturation, hybridization (annealing), andpolymerase extension (elongation) can be repeated as often as needed, inorder to obtain relatively high concentrations of a segment of thedesired target sequence.

The length of the segment of the desired target sequence is determinedby the relative positions of the primers with respect to each other,and, therefore, this length is a controllable parameter. Because thedesired segments of the target sequence become the dominant sequences(in terms of concentration) in the mixture, they are said to be“PCR-amplified.”

Ligase Chain Reaction (LCR or LAR): The ligase chain reaction [LCR;sometimes referred to as “Ligase Amplification Reaction” (LAR)] hasdeveloped into a well-recognized alternative method of amplifyingnucleic acids. In LCR, four oligonucleotides, two adjacentoligonucleotides which uniquely hybridize to one strand of target DNA,and a complementary set of adjacent oligonucleotides, which hybridize tothe opposite strand are mixed and DNA ligase is added to the mixture.Provided that there is complete complementarity at the junction, ligasewill covalently link each set of hybridized molecules. Importantly, inLCR, two probes are ligated together only when they base-pair withsequences in the target sample, without gaps or mismatches. Repeatedcycles of denaturation, and ligation amplify a short segment of DNA. LCRhas also been used in combination with PCR to achieve enhanced detectionof single-base changes: see for example Segev, PCT Publication No.WO9001069 A1 (1990). However, because the four oligonucleotides used inthis assay can pair to form two short ligatable fragments, there is thepotential for the generation of target-independent background signal.The use of LCR for mutant screening is limited to the examination ofspecific nucleic acid positions.

Self-Sustained Synthetic Reaction (3SR/NASBA): The self-sustainedsequence replication reaction (3SR) is a transcription-based in vitroamplification system that can exponentially amplify RNA sequences at auniform temperature. The amplified RNA can then be utilized for mutationdetection. In this method, an oligonucleotide primer is used to add aphage RNA polymerase promoter to the 5′ end of the sequence of interest.In a cocktail of enzymes and substrates that includes a second primer,reverse transcriptase, RNase H, RNA polymerase and ribo- anddeoxyribonucleoside triphosphates, the target sequence undergoesrepeated rounds of transcription, cDNA synthesis and second-strandsynthesis to amplify the area of interest. The use of 3SR to detectmutations is kinetically limited to screening small segments of DNA(e.g., 200-300 base pairs).

Q-Beta (Qβ) Replicase: In this method, a probe which recognizes thesequence of interest is attached to the replicatable RNA template for Qβreplicase. A previously identified major problem with false positivesresulting from the replication of unhybridized probes has been addressedthrough use of a sequence-specific ligation step. However, availablethermostable DNA ligases are not effective on this RNA substrate, so theligation must be performed by T4 DNA ligase at low temperatures (37degrees C.). This prevents the use of high temperature as a means ofachieving specificity as in the LCR, the ligation event can be used todetect a mutation at the junction site, but not elsewhere.

A successful diagnostic method must be very specific. A straight-forwardmethod of controlling the specificity of nucleic acid hybridization isby controlling the temperature of the reaction. While the 3SR/NASBA, andQβ systems are all able to generate a large quantity of signal, one ormore of the enzymes involved in each cannot be used at high temperature(i.e., >55 degrees C.). Therefore the reaction temperatures cannot beraised to prevent non-specific hybridization of the probes. If probesare shortened in order to make them melt more easily at lowtemperatures, the likelihood of having more than one perfect match in acomplex genome increases. For these reasons, PCR and LCR currentlydominate the research field in detection technologies.

The basis of the amplification procedure in the PCR and LCR is the factthat the products of one cycle become usable templates in all subsequentcycles, consequently doubling the population with each cycle. The finalyield of any such doubling system can be expressed as: (1+X)^(n)=y,where “X” is the mean efficiency (percent copied in each cycle), “n” isthe number of cycles, and “y” is the overall efficiency, or yield of thereaction. If every copy of a target DNA is utilized as a template inevery cycle of a polymerase chain reaction, then the mean efficiency is100%. If 20 cycles of PCR are performed, then the yield will be 2²⁰, or1,048,576 copies of the starting material. If the reaction conditionsreduce the mean efficiency to 85%, then the yield in those 20 cycleswill be only 1.85²⁰, or 220,513 copies of the starting material. Inother words, a PCR running at 85% efficiency will yield only 21% as muchfinal product, compared to a reaction running at 100% efficiency. Areaction that is reduced to 50% mean efficiency will yield less than 1%of the possible product.

In practice, routine polymerase chain reactions rarely achieve thetheoretical maximum yield, and PCRs are usually run for more than 20cycles to compensate for the lower yield. At 50% mean efficiency, itwould take 34 cycles to achieve the million-fold amplificationtheoretically possible in 20, and at lower efficiencies, the number ofcycles required becomes prohibitive. In addition, any backgroundproducts that amplify with a better mean efficiency than the intendedtarget will become the dominant products.

Also, many variables can influence the mean efficiency of PCR, includingtarget DNA length and secondary structure, primer length and design,primer and dNTP concentrations, and buffer composition, to name but afew. Contamination of the reaction with exogenous DNA (e.g., DNA spilledonto lab surfaces) or cross-contamination is also a major consideration.Reaction conditions must be carefully optimized for each differentprimer pair and target sequence, and the process can take days, even foran experienced investigator. The laboriousness of this process,including numerous technical considerations and other factors, presentsa significant drawback to using PCR in the clinical setting. Indeed, PCRhas yet to penetrate the clinical market in a significant way. The sameconcerns arise with LCR, as LCR must also be optimized to use differentoligonucleotide sequences for each target sequence. In addition, bothmethods require expensive equipment, capable of precise temperaturecycling.

Many applications of nucleic acid detection technologies, such as instudies of allelic variation, involve not only detection of a specificsequence in a complex background, but also the discrimination betweensequences with few, or single, nucleotide differences. One method of thedetection of allele-specific variants by PCR is based upon the fact thatit is difficult for Taq polymerase to synthesize a DNA strand when thereis a mismatch between the template strand and the 3′ end of the primer.An allele-specific variant may be detected by the use of a primer thatis perfectly matched with only one of the possible alleles; the mismatchto the other allele acts to prevent the extension of the primer, therebypreventing the amplification of that sequence. This method has asubstantial limitation in that the base composition of the mismatchinfluences the ability to prevent extension across the mismatch, andcertain mismatches do not prevent extension or have only a minimaleffect.

A similar 3′-mismatch strategy is used with greater effect to preventligation in the LCR. Any mismatch effectively blocks the action of thethermostable ligase, but LCR still has the drawback oftarget-independent background ligation products initiating theamplification. Moreover, the combination of PCR with subsequent LCR toidentify the nucleotides at individual positions is also a clearlycumbersome proposition for the clinical laboratory.

The direct detection method according to various embodiments of thepresent invention may be, for example a cycling probe reaction (CPR) ora branched DNA analysis.

When a sufficient amount of a nucleic acid to be detected is available,there are advantages to detecting that sequence directly, instead ofmaking more copies of that target, (e.g., as in PCR and LCR). Mostnotably, a method that does not amplify the signal exponentially is moreamenable to quantitative analysis. Even if the signal is enhanced byattaching multiple dyes to a single oligonucleotide, the correlationbetween the final signal intensity and amount of target is direct. Sucha system has an additional advantage that the products of the reactionwill not themselves promote further reaction, so contamination of labsurfaces by the products is not as much of a concern. Recently devisedtechniques have sought to eliminate the use of radioactivity and/orimprove the sensitivity in automatable formats. Two examples are the“Cycling Probe Reaction” (CPR), and “Branched DNA” (bDNA).

Cycling probe reaction (CPR): The cycling probe reaction (CPR), uses along chimeric oligonucleotide in which a central portion is made of RNAwhile the two termini are made of DNA. Hybridization of the probe to atarget DNA and exposure to a thermostable RNase H causes the RNA portionto be digested. This destabilizes the remaining DNA portions of theduplex, releasing the remainder of the probe from the target DNA andallowing another probe molecule to repeat the process. The signal, inthe form of cleaved probe molecules, accumulates at a linear rate. Whilethe repeating process increases the signal, the RNA portion of theoligonucleotide is vulnerable to RNases that may carried through samplepreparation.

Branched DNA: Branched DNA (bDNA), involves oligonucleotides withbranched structures that allow each individual oligonucleotide to carry35 to 40 labels (e.g., alkaline phosphatase enzymes). While thisenhances the signal from a hybridization event, signal from non-specificbinding is similarly increased.

The detection of at least one sequence change according to variousembodiments of the present invention may be accomplished by, for examplerestriction fragment length polymorphism (RFLP analysis), allelespecific oligonucleotide (ASO) analysis, Denaturing/Temperature GradientGel Electrophoresis (DGGE/TGGE), Single-Strand Conformation Polymorphism(SSCP) analysis or Dideoxy fingerprinting (ddF).

The demand for tests which allow the detection of specific nucleic acidsequences and sequence changes is growing rapidly in clinicaldiagnostics. As nucleic acid sequence data for genes from humans andpathogenic organisms accumulates, the demand for fast, cost-effective,and easy-to-use tests for as yet mutations within specific sequences israpidly increasing.

A handful of methods have been devised to scan nucleic acid segments formutations. One option is to determine the entire gene sequence of eachtest sample (e.g., a bacterial isolate). For sequences underapproximately 600 nucleotides, this may be accomplished using amplifiedmaterial (e.g., PCR reaction products). This avoids the time and expenseassociated with cloning the segment of interest. However, specializedequipment and highly trained personnel are required, and the method istoo labor-intense and expensive to be practical and effective in theclinical setting.

In view of the difficulties associated with sequencing, a given segmentof nucleic acid may be characterized on several other levels. At thelowest resolution, the size of the molecule can be determined byelectrophoresis by comparison to a known standard run on the same gel. Amore detailed picture of the molecule may be achieved by cleavage withcombinations of restriction enzymes prior to electrophoresis, to allowconstruction of an ordered map. The presence of specific sequenceswithin the fragment can be detected by hybridization of a labeled probe,or the precise nucleotide sequence can be determined by partial chemicaldegradation or by primer extension in the presence of chain-terminatingnucleotide analogs.

Restriction fragment length polymorphism (RFLP): For detection ofsingle-base differences between like sequences, the requirements of theanalysis are often at the highest level of resolution. For cases inwhich the position of the nucleotide in question is known in advance,several methods have been developed for examining single base changeswithout direct sequencing. For example, if a mutation of interesthappens to fall within a restriction recognition sequence, a change inthe pattern of digestion can be used as a diagnostic tool (e.g.,restriction fragment length polymorphism [RFLP] analysis).

Single point mutations have been also detected by the creation ordestruction of RFLPs. Mutations are detected and localized by thepresence and size of the RNA fragments generated by cleavage at themismatches. Single nucleotide mismatches in DNA heteroduplexes are alsorecognized and cleaved by some chemicals, providing an alternativestrategy to detect single base substitutions, generically named the“Mismatch Chemical Cleavage” (MCC). However, this method requires theuse of osmium tetroxide and piperidine, two highly noxious chemicalswhich are not suited for use in a clinical laboratory.

RFLP analysis suffers from low sensitivity and requires a large amountof sample. When RFLP analysis is used for the detection of pointmutations, it is, by its nature, limited to the detection of only thosesingle base changes which fall within a restriction sequence of a knownrestriction endonuclease. Moreover, the majority of the availableenzymes have 4 to 6 base-pair recognition sequences, and cleave toofrequently for many large-scale DNA manipulations. Thus, it isapplicable only in a small fraction of cases, as most mutations do notfall within such sites.

A handful of rare-cutting restriction enzymes with 8 base-pairspecificities have been isolated and these are widely used in geneticmapping, but these enzymes are few in number, are limited to therecognition of G+C-rich sequences, and cleave at sites that tend to behighly clustered. Recently, endonucleases encoded by group I intronshave been discovered that might have greater than 12 base-pairspecificity, but again, these are few in number.

Allele specific oligonucleotide (ASO): If the change is not in arecognition sequence, then allele-specific oligonucleotides (ASOs), canbe designed to hybridize in proximity to the mutated nucleotide, suchthat a primer extension or ligation event can bused as the indicator ofa match or a mis-match. Hybridization with radioactively labeled allelicspecific oligonucleotides (ASO) also has been applied to the detectionof specific point mutations. The method is based on the differences inthe melting temperature of short DNA fragments differing by a singlenucleotide. Stringent hybridization and washing conditions candifferentiate between mutant and wild-type alleles. The ASO approachapplied to PCR products also has been extensively utilized by variousresearchers to detect and characterize point mutations in ras genes andgsp/gip oncogenes. Because of the presence of various nucleotide changesin multiple positions, the ASO method requires the use of manyoligonucleotides to cover all possible oncogenic mutations.

With either of the techniques described above (i.e., RFLP and ASO), theprecise location of the suspected mutation must be known in advance ofthe test. That is to say, they are inapplicable when one needs to detectthe presence of a mutation within a gene or sequence of interest.

Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE): Twoother methods rely on detecting changes in electrophoretic mobility inresponse to minor sequence changes. One of these methods, termed“Denaturing Gradient Gel Electrophoresis” (DGGE) is based on theobservation that slightly different sequences will display differentpatterns of local melting when electrophoretically resolved on agradient gel. In this manner, variants can be distinguished, asdifferences in melting properties of homoduplexes versus heteroduplexesdiffering in a single nucleotide can detect the presence of mutations inthe target sequences because of the corresponding changes in theirelectrophoretic mobilities. The fragments to be analyzed, usually PCRproducts, are “clamped” at one end by a long stretch of G-C base pairs(30-80) to allow complete denaturation of the sequence of interestwithout complete dissociation of the strands. The attachment of a GC“clamp” to the DNA fragments increases the fraction of mutations thatcan be recognized by DGGE. Attaching a GC clamp to one primer iscritical to ensure that the amplified sequence has a low dissociationtemperature. Modifications of the technique have been developed, usingtemperature gradients, and the method can be also applied to RNA:RNAduplexes.

Limitations on the utility of DGGE include the requirement that thedenaturing conditions must be optimized for each type of DNA to betested. Furthermore, the method requires specialized equipment toprepare the gels and maintain the needed high temperatures duringelectrophoresis. The expense associated with the synthesis of theclamping tail on one oligonucleotide for each sequence to be tested isalso a major consideration. In addition, long running times are requiredfor DGGE. The long running time of DGGE was shortened in a modificationof DGGE called constant denaturant gel electrophoresis (CDGE). CDGErequires that gels be performed under different denaturant conditions inorder to reach high efficiency for the detection of mutations.

A technique analogous to DGGE, termed temperature gradient gelelectrophoresis (TGGE), uses a thermal gradient rather than a chemicaldenaturant gradient. TGGE requires the use of specialized equipmentwhich can generate a temperature gradient perpendicularly orientedrelative to the electrical field. TGGE can detect mutations inrelatively small fragments of DNA therefore scanning of large genesegments requires the use of multiple PCR products prior to running thegel.

Single-Strand Conformation Polymorphism (SSCP): Another common method,called “Single-Strand Conformation Polymorphism” (SSCP) was developed byHayashi, Sekya and colleagues and is based on the observation thatsingle strands of nucleic acid can take on characteristic conformationsin non-denaturing conditions, and these conformations influenceelectrophoretic mobility. The complementary strands assume sufficientlydifferent structures that one strand may be resolved from the other.Changes in sequences within the fragment will also change theconformation, consequently altering the mobility and allowing this to beused as an assay for sequence variations.

The SSCP process involves denaturing a DNA segment (e.g., a PCR product)that is labeled on both strands, followed by slow electrophoreticseparation on a non-denaturing polyacrylamide gel, so thatintra-molecular interactions can form and not be disturbed during therun. This technique is extremely sensitive to variations in gelcomposition and temperature. A serious limitation of this method is therelative difficulty encountered in comparing data generated in differentlaboratories, under apparently similar conditions.

Dideoxy fingerprinting (ddF): The dideoxy fingerprinting (ddF) isanother technique developed to scan genes for the presence of mutations.The ddF technique combines components of Sanger dideoxy sequencing withSSCP. A dideoxy sequencing reaction is performed using one dideoxyterminator and then the reaction products are electrophoresed onnondenaturing polyacrylamide gels to detect alterations in mobility ofthe termination segments as in SSCP analysis. While ddF is animprovement over SSCP in terms of increased sensitivity, ddF requiresthe use of expensive dideoxynucleotides and this technique is stilllimited to the analysis of fragments of the size suitable for SSCP(i.e., fragments of 200-300 bases for optimal detection of mutations).

In addition to the above limitations, all of these methods are limitedas to the size of the nucleic acid fragment that can be analyzed. Forthe direct sequencing approach, sequences of greater than 600 base pairsrequire cloning, with the consequent delays and expense of eitherdeletion sub-cloning or primer walking, in order to cover the entirefragment. SSCP and DGGE have even more severe size limitations. Becauseof reduced sensitivity to sequence changes, these methods are notconsidered suitable for larger fragments. Although SSCP is reportedlyable to detect 90% of single-base substitutions within a 200 base-pairfragment, the detection drops to less than 50% for 400 base pairfragments. Similarly, the sensitivity of DGGE decreases as the length ofthe fragment reaches 500 base-pairs. The ddF technique, as a combinationof direct sequencing and SSCP, is also limited by the relatively smallsize of the DNA that can be screened.

According to a one embodiment of the present invention the step ofsearching for any of the nucleic acid sequences described here, in tumorcells or in cells derived from a cancer patient is effected by anysuitable technique, including, but not limited to, nucleic acidsequencing, polymerase chain reaction, ligase chain reaction,self-sustained synthetic reaction, Qβ-Replicase, cycling probe reaction,branched DNA, restriction fragment length polymorphism analysis,mismatch chemical cleavage, heteroduplex analysis, allele-specificoligonucleotides, denaturing gradient gel electrophoresis, constantdenaturant gel electrophoresis, temperature gradient gel electrophoresisand dideoxy fingerprinting.

Detection may also optionally be performed with a chip or other suchdevice. The nucleic acid sample which includes the candidate region tobe analyzed is preferably isolated, amplified and labeled with areporter group. This reporter group can be a fluorescent group such asphycoerythrin. The labeled nucleic acid is then incubated with theprobes immobilized on the chip using a fluidics station. describe thefabrication of fluidics devices and particularly microcapillary devices,in silicon and glass substrates.

Once the reaction is completed, the chip is inserted into a scanner andpatterns of hybridization are detected. The hybridization data iscollected, as a signal emitted from the reporter groups alreadyincorporated into the nucleic acid, which is now bound to the probesattached to the chip. Since the sequence and position of each probeimmobilized on the chip is known, the identity of the nucleic acidhybridized to a given probe can be determined.

It will be appreciated that when utilized along with automatedequipment, the above described detection methods can be used to screenmultiple samples for a disease and/or pathological condition bothrapidly and easily.

Amino Acid Sequences and Peptides

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidue is an analog or mimetic of a corresponding naturally occurringamino acid, as well as to naturally occurring amino acid polymers.Polypeptides can be modified, e.g., by the addition of carbohydrateresidues to form glycoproteins. The terms “polypeptide,” “peptide” and“protein” include glycoproteins, as well as non-glycoproteins.

Polypeptide products can be biochemically synthesized such as byemploying standard solid phase techniques. Such methods include but arenot limited to exclusive solid phase synthesis, partial solid phasesynthesis methods, fragment condensation, classical solution synthesis.These methods are preferably used when the peptide is relatively short(i.e., 10 kDa) and/or when it cannot be produced by recombinanttechniques (i.e., not encoded by a nucleic acid sequence) and thereforeinvolves different chemistry.

Solid phase polypeptide synthesis procedures are well known in the artand further described by John Morrow Stewart and Janis Dillaha Young,Solid Phase Peptide Syntheses (2nd Ed., Pierce Chemical Company, 1984).

Synthetic polypeptides can optionally be purified by preparative highperformance liquid chromatography [Creighton T. (1983) Proteins,structures and molecular principles. WH Freeman and Co. N.Y.], afterwhich their composition can be confirmed via amino acid sequencing.

In cases where large amounts of a polypeptide are desired, it can begenerated using recombinant techniques such as described by Bitter etal., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990)Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514,Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J.3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al.(1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988,Methods for Plant Molecular Biology, Academic Press, NY, Section VIII,pp 421-463.

The present invention also encompasses polypeptides encoded by thepolynucleotide sequences of the present invention, as well aspolypeptides according to the amino acid sequences described herein. Thepresent invention also encompasses homologues of these polypeptides,such homologues can be at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 95% or more say 100% homologous to the amino acid sequences setforth below, as can be determined using BlastP software of the NationalCenter of Biotechnology Information (NCBI) using default parameters,optionally and preferably including the following: filtering on (thisoption filters repetitive or low-complexity sequences from the queryusing the Seg (protein) program), scoring matrix is BLOSUM62 forproteins, word size is 3, E value is 10, gap costs are 11, 1(initialization and extension), and number of alignments shown is 50.Preferably, nucleic acid sequence homology/identity is determined byusing BlastN software of the National Center of BiotechnologyInformation (NCBI) using default parameters, which preferably includeusing the DUST filter program, and also preferably include having an Evalue of 10, filtering low complexity sequences and a word size of 11.Finally, the present invention also encompasses fragments of the abovedescribed polypeptides and polypeptides having mutations, such asdeletions, insertions or substitutions of one or more amino acids,either naturally occurring or artificially induced, either randomly orin a targeted fashion.

It will be appreciated that peptides identified according the presentinvention may be degradation products, synthetic peptides or recombinantpeptides as well as peptidomimetics, typically, synthetic peptides andpeptoids and semipeptoids which are peptide analogs, which may have, forexample, modifications rendering the peptides more stable while in abody or more capable of penetrating into cells.

In addition to the above, the peptides of the present invention may alsoinclude one or more modified amino acids or one or more non-amino acidmonomers (e.g. fatty acids, complex carbohydrates etc).

As used herein in the specification and in the claims section below theterm “amino acid” or “amino acids” is understood to include the 20naturally occurring amino acids; those amino acids often modifiedpost-translationally in vivo, including, for example, hydroxyproline,phosphoserine and phosphothreonine; and other unusual amino acidsincluding, but not limited to, 2-aminoadipic acid, hydroxylysine,isodesmosine, nor-valine, nor-leucine and ornithine. Furthermore, theterm “amino acid” includes both D- and L-amino acids. Non-conventionalor modified amino acids can be incorporated in the polypeptides of thisinvention as well, as will be known to one skilled in the art.

Since the peptides of the present invention are utilized, in someembodiments, in diagnostics which require the peptides to be in solubleform, the peptides of the present invention may include one or morenon-natural or natural polar amino acids, including but not limited toserine and threonine which are capable of increasing peptide solubilitydue to their hydroxyl-containing side chain.

The peptides of the present invention may be utilized in a linear form,although it will be appreciated that in cases where cyclicization doesnot severely interfere with peptide characteristics, cyclic forms of thepeptide can also be utilized.

The peptides of present invention can be biochemically synthesized suchas by using standard solid phase techniques. These methods includeexclusive solid phase synthesis well known in the art, partial solidphase synthesis methods, fragment condensation, classical solutionsynthesis. These methods are preferably used when the peptide isrelatively short (i.e., 10 kDa) and/or when it cannot be produced byrecombinant techniques (i.e., not encoded by a nucleic acid sequence)and therefore involves different chemistry.

Synthetic peptides can be purified by preparative high performanceliquid chromatography and the composition of which can be confirmed viaamino acid sequencing.

In cases where large amounts of the peptides of the present inventionare desired, the peptides of the present invention can be generatedusing recombinant techniques such as described by Bitter et al., (1987)Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods inEnzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsuet al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J.3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al.(1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988,Methods for Plant Molecular Biology, Academic Press, NY, Section VIII,pp 421-463 and also as described above.

Antibodies:

“Antibody” refers to a polypeptide ligand that is preferablysubstantially encoded by an immunoglobulin gene or immunoglobulin genes,or fragments thereof, which specifically binds and recognizes an epitope(e.g., an antigen). The recognized immunoglobulin genes include thekappa and lambda light chain constant region genes, the alpha, gamma,delta, epsilon and mu heavy chain constant region genes, and themyriad-immunoglobulin variable region genes. Antibodies exist, e.g., asintact immunoglobulins or as a number of well characterized fragmentsproduced by digestion with various peptidases. This includes, e.g., Fab′and F(ab)′2 fragments. The term “antibody,” as used herein, alsoincludes antibody fragments either produced by the modification of wholeantibodies or those synthesized de novo using recombinant DNAmethodologies. It also includes polyclonal antibodies, monoclonalantibodies, chimeric antibodies, humanized antibodies, or single chainantibodies. “Fc” portion of an antibody refers to that portion of animmunoglobulin heavy chain that comprises one or more heavy chainconstant region domains, CH1, CH2 and CH3, but does not include theheavy chain variable region.

The functional fragments of antibodies, such as Fab, F(ab′)2, and Fvthat are capable of binding to macrophages, are described as follows:(1) Fab, the fragment which contains a monovalent antigen-bindingfragment of an antibody molecule, can be produced by digestion of wholeantibody with the enzyme papain to yield an intact light chain and aportion of one heavy chain; (2) Fab′, the fragment of an antibodymolecule that can be obtained by treating whole antibody with pepsin,followed by reduction, to yield an intact light chain and a portion ofthe heavy chain; two Fab′ fragments are obtained per antibody molecule;(3) (Fab′)₂, the fragment of the antibody that can be obtained bytreating whole antibody with the enzyme pepsin without subsequentreduction; F(ab′)2 is a dimer of two Fab′ fragments held together by twodisulfide bonds; (4) Fv, defined as a genetically engineered fragmentcontaining the variable region of the light chain and the variableregion of the heavy chain expressed as two chains; and (5) Single chainantibody (“SCA”), a genetically engineered molecule containing thevariable region of the light chain and the variable region of the heavychain, linked by a suitable polypeptide linker as a genetically fusedsingle chain molecule.

Methods of producing polyclonal and monoclonal antibodies as well asfragments thereof are well known in the art (See for example, Harlow andLane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory,New York, 1988, incorporated herein by reference).

Monoclonal antibody development may optionally be performed according toany method that is known in the art. The method described below isprovided for the purposes of description only and is not meant to belimiting in any way.

Antibody Engineering in Phage Display Libraries:

Antibodies of this invention may be prepared through the use of phagedisplay libraries, as is known in the art, for example, as described inPCT Application No. WO 94/18219, U.S. Pat. No. 6,096,551, both of whichare hereby fully incorporated by reference, The method involves inducingmutagenesis in a complementarity determining region (CDR) of animmunoglobulin light chain gene for the purpose of producing light chaingene libraries for use in combination with heavy chain genes and genelibraries to produce antibody libraries of diverse and novelimmuno-specificities. The method comprises amplifying a CDR portion ofan immunoglobulin light chain gene by polymerase chain reaction (PCR)using a PCR primer oligonucleotide. The resultant gene portions areinserted into phagemids for production of a phage display library,wherein the engineered light chains are displayed by the phages, forexample for testing their binding specificity.

Antibody fragments according to the present invention can be prepared byproteolytic hydrolysis of the antibody or by expression in E. coli ormammalian cells (e.g. Chinese hamster ovary cell culture or otherprotein expression systems) of DNA encoding the fragment. Antibodyfragments can be obtained by pepsin or papain digestion of wholeantibodies by conventional methods. For example, antibody fragments canbe produced by enzymatic cleavage of antibodies with pepsin to provide a5S fragment denoted F(ab′)2. This fragment can be further cleaved usinga thiol reducing agent, and optionally a blocking group for thesulfhydryl groups resulting from cleavage of disulfide linkages, toproduce 3.5S Fab′ monovalent fragments. Alternatively, an enzymaticcleavage using Papain produces two monovalent Fab′ fragments and an Fcfragment directly. These methods are described, for example, byGoldenberg, U.S. Pat. Nos. 4,036,945 and 4,331,647, and referencescontained therein, which patents are hereby incorporated by reference intheir entirety. See also Porter, R. R. [Biochem. J. 73: 119-126 (1959)].Other methods of cleaving antibodies, such as separation of heavy chainsto form monovalent light-heavy chain fragments, further cleavage offragments, or other enzymatic, chemical, or genetic techniques may alsobe used, so long as the fragments bind to the antigen that is recognizedby the intact antibody.

Fv fragments comprise an association of VH and VL chains. Thisassociation may be noncovalent, as described in Inbar et al. [Proc.Nat'l Acad. Sci. USA 69:2659-62 (1972)]. Alternatively, the variablechains can be linked by an intermolecular disulfide bond or cross-linkedby chemicals such as glutaraldehyde. Preferably, the Fv fragmentscomprise VH and VL chains connected by a peptide linker. Thesesingle-chain antigen binding proteins (sFv) are prepared by constructinga structural gene comprising DNA sequences encoding the VH and VLdomains connected by an oligonucleotide. The structural gene is insertedinto an expression vector, which is subsequently introduced into a hostcell such as E. coli. The recombinant host cells synthesize a singlepolypeptide chain with a linker peptide bridging the two V domains. AscFv antibody fragment is an engineered antibody derivative thatincludes heavy- and light chain variable regions joined by a peptidelinker. The minimal size of antibody molecules are those that stillcomprise the complete antigen binding site. ScFv antibody fragments arepotentially more effective than unmodified IgG antibodies. The reducedsize of 27-30 kDa permits them to penetrate tissues and solid tumorsmore readily. Methods for producing sFvs are described, for example, by[Whitlow and Filpula, Methods 2: 97-105 (1991); Bird et al., Science242:423-426 (1988); Pack et al., Bio/Technology 11:1271-77 (1993); andU.S. Pat. No. 4,946,778, which is hereby incorporated by reference inits entirety.

Another form of an antibody fragment is a peptide coding for a singlecomplementarity-determining region (CDR). CDR peptides (“minimalrecognition units”) can be obtained by constructing genes encoding theCDR of an antibody of interest. Such genes are prepared, for example, byusing the polymerase chain reaction to synthesize the variable regionfrom RNA of antibody-producing cells. See, for example, Larrick and Fry[Methods, 2: 106-10 (1991)]. Optionally, there may be 1, 2 or 3 CDRs ofdifferent chains, but preferably there are 3 CDRs of 1 chain. The chaincould be the heavy or the light chain.

Humanized forms of non-human (e.g., murine) antibodies, are chimericmolecules of immunoglobulins, immunoglobulin chains or fragments thereof(such as Fv, Fab, Fab′, F(ab′) or other antigen-binding subsequences ofantibodies) which contain minimal sequence derived from non-humanimmunoglobulin, or fragments thereof may comprise the antibodies of thisinvention. Humanized antibodies are well known in the art. Methods forhumanizing non-human antibodies are well known in the art, for example,as described in Winter and co-workers [Jones et al., Nature, 321:522-525(1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al.,Science, 239:1534-1536 (1988)], U.S. Pat. No. 4,816,567, Hoogenboom andWinter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol.,222:581 (1991), Cole et al., Monoclonal Antibodies and Cancer Therapy,Alan R. Liss, p. 77 (1985), Boerner et al., J. Immunol., 147(1):86-95(1991), U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126;5,633,425; 5,661,016, and in the following scientific publications:Marks et al., Bio/Technology 10: 779-783 (1992); Lonberg et al., Nature368: 856-859 (1994); Morrison, Nature 368 812-13 (1994); Fishwild etal., Nature Biotechnology 14, 845-51 (1996); Neuberger, NatureBiotechnology 14: 826 (1996); and Lonberg and Huszar, Intern. Rev.Immunol. 13, 65-93 (1995), all of which are incorporated herein byreference.

Preferably, the antibody of this aspect of the present inventionspecifically binds at least one epitope of the polypeptide variants ofthe present invention. As used herein, the term “epitope” refers to anyantigenic determinant on an antigen to which the paratope of an antibodybinds.

Epitopic determinants usually consist of chemically active surfacegroupings of molecules such as amino acids or carbohydrate side chainsand usually have specific three dimensional structural characteristics,as well as specific charge characteristics.

Optionally, a unique epitope may be created in a variant due to a changein one or more post-translational modifications, including but notlimited to glycosylation and/or phosphorylation, as described below.Such a change may also cause a new epitope to be created, for examplethrough removal of glycosylation at a particular site.

An epitope according to the present invention may also optionallycomprise part or all of a unique sequence portion of a variant accordingto the present invention in combination with at least one other portionof the variant which is not contiguous to the unique sequence portion inthe linear polypeptide itself, yet which are able to form an epitope incombination. One or more unique sequence portions may optionally combinewith one or more other non-contiguous portions of the variant (includinga portion which may have high homology to a portion of the knownprotein) to form an epitope.

Immunoassays

In another embodiment of the present invention, an immunoassay can beused to qualitatively or quantitatively detect and analyze markers in asample. This method comprises: providing an antibody that specificallybinds to a marker; contacting a sample with the antibody; and detectingthe presence of a complex of the antibody bound to the marker in thesample.

To prepare an antibody that specifically binds to a marker, purifiedprotein markers can be used. Antibodies that specifically bind to aprotein marker can be prepared using any suitable methods known in theart.

After the antibody is provided, a marker can be detected and/orquantified using any of a number of well recognized immunologicalbinding assays. Useful assays include, for example, an enzyme immuneassay (EIA) such as enzyme-linked immunosorbent assay (ELISA), aradioimmune assay (RIA), a Western blot assay, or a slot blot assay see,e.g., U.S. Pat. Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168).Generally, a sample obtained from a subject can be contacted with theantibody that specifically binds the marker.

Optionally, the antibody can be fixed to a solid support to facilitatewashing and subsequent isolation of the complex, prior to contacting theantibody with a sample. Examples of solid supports include but are notlimited to glass or plastic in the form of, e.g., a microtiter plate, astick, a bead, or a microbead. Antibodies can also be attached to asolid support.

After incubating the sample with antibodies, the mixture is washed andthe antibody-marker complex formed can be detected. This can beaccomplished by incubating the washed mixture with a detection reagent.Alternatively, the marker in the sample can be detected using anindirect assay, wherein, for example, a second, labeled antibody is usedto detect bound marker-specific antibody, and/or in a competition orinhibition assay wherein, for example, a monoclonal antibody which bindsto a distinct epitope of the marker are incubated simultaneously withthe mixture.

Throughout the assays, incubation and/or washing steps may be requiredafter each combination of reagents. Incubation steps can vary from about5 seconds to several hours, preferably from about 5 minutes to about 24hours. However, the incubation time will depend upon the assay format,marker, volume of solution, concentrations and the like. Usually theassays will be carried out at ambient temperature, although they can beconducted over a range of temperatures, such as 10° C. to 40° C.

The immunoassay can be used to determine a test amount of a marker in asample from a subject. First, a test amount of a marker in a sample canbe detected using the immunoassay methods described above. If a markeris present in the sample, it will form an antibody-marker complex withan antibody that specifically binds the marker under suitable incubationconditions described above. The amount of an antibody-marker complex canoptionally be determined by comparing to a standard. As noted above, thetest amount of marker need not be measured in absolute units, as long asthe unit of measurement can be compared to a control amount and/orsignal.

In some embodiments, antibodies which specifically interact with thepolypeptides of the present invention and not with wild type proteins orother isoforms thereof, are used. Such antibodies are directed, forexample, to the unique sequence portions of the polypeptide variants ofthe present invention, including but not limited to bridges, heads,tails and insertions described in greater detail below. Some embodimentsof antibodies according to the present invention are described ingreater detail with regard to the section entitled “Antibodies”.

Radio-immunoassay (RIA): In one version, this method involvesprecipitation of the desired substrate and in the methods detailedhereinbelow, with a specific antibody and radiolabelled antibody bindingprotein (e.g., protein A labeled with I¹²⁵) immobilized on aprecipitable carrier such as agarose beads. The number of counts in theprecipitated pellet is proportional to the amount of substrate.

In an alternate version of the RIA, a labeled substrate and anunlabelled antibody binding protein are employed. A sample containing anunknown amount of substrate is added in varying amounts. The decrease inprecipitated counts from the labeled substrate is proportional to theamount of substrate in the added sample.

Enzyme linked immunosorbent assay (ELISA): This method involves fixationof a sample (e.g., fixed cells or a proteinaceous solution) containing aprotein substrate to a surface such as a well of a microtiter plate. Asubstrate specific antibody coupled to an enzyme is applied and allowedto bind to the substrate. Presence of the antibody is then detected andquantitated by a colorimetric reaction employing the enzyme coupled tothe antibody. Enzymes commonly employed in this method includehorseradish peroxidase and alkaline phosphatase. If well calibrated andwithin the linear range of response, the amount of substrate present inthe sample is proportional to the amount of color produced. A substratestandard is generally employed to improve quantitative accuracy.

Western blot: This method involves separation of a substrate from otherprotein by means of an acrylamide gel followed by transfer of thesubstrate to a membrane (e.g., nylon or PVDF). Presence of the substrateis then detected by antibodies specific to the substrate, which are inturn detected by antibody binding reagents. Antibody binding reagentsmay be, for example, protein A, or other antibodies. Antibody bindingreagents may be radiolabelled or enzyme linked as described hereinabove.Detection may be by autoradiography, colorimetric reaction orchemiluminescence. This method allows both quantitation of an amount ofsubstrate and determination of its identity by a relative position onthe membrane which is indicative of a migration distance in theacrylamide gel during electrophoresis.

Immunohistochemical analysis: This method involves detection of asubstrate in situ in fixed cells by substrate specific antibodies. Thesubstrate specific antibodies may be enzyme linked or linked tofluorophores. Detection is by microscopy and subjective evaluation. Ifenzyme linked antibodies are employed, a colorimetric reaction may berequired.

Fluorescence activated cell sorting (FACS): This method involvesdetection of a substrate in situ in cells by substrate specificantibodies. The substrate specific antibodies are linked tofluorophores. Detection is by means of a cell sorting machine whichreads the wavelength of light emitted from each cell as it passesthrough a light beam. This method may employ two or more antibodiessimultaneously.

Radio-Imaging Methods

These methods include but are not limited to, positron emissiontomography (PET) single photon emission computed tomography (SPECT).Both of these techniques are non-invasive, and can be used to detectand/or measure a wide variety of tissue events and/or functions, such asdetecting cancerous cells for example. Unlike PET, SPECT can optionallybe used with two labels simultaneously. SPECT has some other advantagesas well, for example with regard to cost and the types of labels thatcan be used. For example, U.S. Pat. No. 6,696,686 describes the use ofSPECT for detection of breast cancer, and is hereby incorporated byreference as if fully set forth herein.

Display Libraries

According to another aspect of the present invention there is provided adisplay library comprising a plurality of display vehicles (such asphages, viruses or bacteria) each displaying at least 6, at least 7, atleast 8, at least 9, at least 10, 10-15, 12-17, 15-20, 15-30 or 20-50consecutive amino acids derived from the polypeptide sequences of thepresent invention.

Methods of constructing such display libraries are well known in theart. Such methods are described in, for example, Young A C, et al., “Thethree-dimensional structures of a polysaccharide binding antibody toCryptococcus neoformans and its complex with a peptide from a phagedisplay library: implications for the identification of peptidemimotopes” J Mol Biol 1997 Dec. 12; 274(4):622-34; Giebel L B et al.“Screening of cyclic peptide phage libraries identifies ligands thatbind streptavidin with high affinities” Biochemistry 1995 Nov. 28;34(47):15430-5; Davies E L et al., “Selection of specific phage-displayantibodies using libraries derived from chicken immunoglobulin genes” JImmunol Methods 1995 Oct. 12; 186(1):125-35; Jones C R T al. “Currenttrends in molecular recognition and bioseparation” J Chromatogr A 1995Jul. 14; 707(1):3-22; Deng S J et al. “Basis for selection of improvedcarbohydrate-binding single-chain antibodies from synthetic genelibraries” Proc Natl Acad Sci USA 1995 May 23; 92(11):4992-6; and Deng SJ et al. “Selection of antibody single-chain variable fragments withimproved carbohydrate binding by phage display” J Biol Chem 1994 Apr. 1;269(13):9533-8, which are incorporated herein by reference.

Theranostics:

The term theranostics describes the use of diagnostic testing todiagnose the disease, choose the correct treatment regime according tothe results of diagnostic testing and/or monitor the patient response totherapy according to the results of diagnostic testing. Theranostictests can be used to select patients for treatments that areparticularly likely to benefit them and unlikely to produceside-effects. They can also provide an early and objective indication oftreatment efficacy in individual patients, so that (if necessary) thetreatment can be altered with a minimum of delay. For example: DAKO andGenentech together created HercepTest and Herceptin (trastuzumab) forthe treatment of breast cancer, the first theranostic test approvedsimultaneously with a new therapeutic drug. In addition to HercepTest(which is an immunohistochemical test), other theranostic tests are indevelopment which use traditional clinical chemistry, immunoassay,cell-based technologies and nucleic acid tests. PPGx's recently launchedTPMT (thiopurine S-methyltransferase) test, which is enabling doctors toidentify patients at risk for potentially fatal adverse reactions to6-mercaptopurine, an agent used in the treatment of leukemia. Also, NovaMolecular pioneered SNP genotyping of the apolipoprotein E gene topredict Alzheimer's disease patients' responses to cholinomimetictherapies and it is now widely used in clinical trials of new drugs forthis indication. Thus, the field of theranostics represents theintersection of diagnostic testing information that predicts theresponse of a patient to a treatment with the selection of theappropriate treatment for that particular patient.

Surrogate Markers:

A surrogate marker is a marker, that is detectable in a laboratoryand/or according to a physical sign or symptom on the patient, and thatis used in therapeutic trials as a substitute for a clinicallymeaningful endpoint. The surrogate marker is a direct measure of how apatient feels, functions, or survives which is expected to predict theeffect of the therapy. The need for surrogate markers mainly arises whensuch markers can be measured earlier, more conveniently, or morefrequently than the endpoints of interest in terms of the effect of atreatment on a patient, which are referred to as the clinical endpoints.Ideally, a surrogate marker should be biologically plausible, predictiveof disease progression and measurable by standardized assays (includingbut not limited to traditional clinical chemistry, immunoassay,cell-based technologies, nucleic acid tests and imaging modalities).

Surrogate endpoints were used first mainly in the cardiovascular area.For example, antihypertensive drugs have been approved based on theireffectiveness in lowering blood pressure. Similarly, in the past,cholesterol-lowering agents have been approved based on their ability todecrease serum cholesterol, not on the direct evidence that theydecrease mortality from atherosclerotic heart disease. The measurementof cholesterol levels is now an accepted surrogate marker ofatherosclerosis. In addition, currently two commonly used surrogatemarkers in HIV studies are CD4+ T cell counts and quantitative plasmaI-V RNA (viral load). In some embodiments of this invention, thepolypeptide/polynucleotide expression pattern may serve as a surrogatemarker for a particular disease, as will be appreciated by one skilledin the art.

Monoclonal Antibody Therapy:

In some embodiments, monoclonal antibodies are useful for theidentification of cancer cells. In some embodiments, monoclonal antibodytherapy is a form of passive immunotherapy useful in cancer treatment.Such antibodies may comprise naked monoclonal antibodies or conjugatedmonoclonal antibodies—joined to a chemotherapy drug, radioactiveparticle, or a toxin (a substance that poisons cells). In someembodiments, the former is directly cytotoxic to the target (cancer)cell, or in another embodiment, stimulates or otherwise participates inan immune response ultimately resulting in the lysis of the target cell.

In some embodiments, the conjugated monoclonal antibodies are joined todrugs, toxins, or radioactive atoms. They are used as delivery vehiclesto take those substances directly to the cancer cells. The MAb acts as ahoming device, circulating in the body until it finds a cancer cell witha matching antigen. It delivers the toxic substance to where it isneeded most, minimizing damage to normal cells in other parts of thebody. Conjugated MAbs are also sometimes referred to as “tagged,”“labeled,” or “loaded” antibodies. MAbs with chemotherapy drugs attachedare generally referred to as chemolabeled. MAbs with radioactiveparticles attached are referred to as radiolabeled, and this type oftherapy is known as radioimmunotherapy (RIT). MAbs attached to toxinsare called immunotoxins.

An illustrative, non-limiting example is provided herein of a method oftreatment of a patient with an antibody to a variant as describedherein, such that the variant is a target of the antibody. A patientwith breast cancer is treated with a radiolabeled humanized antibodyagainst an appropriate breast cancer target as described herein. Thepatient is optionally treated with a dosage of labeled antibody rangingfrom 10 to 30 mCi. Of course any type of therapeutic label mayoptionally be used.

The following sections relate to Candidate Marker Examples. It should benoted that Table numbering is restarted within each Example, whichstarts with the words “Description for Cluster”.

Candidate Marker Examples Section

This Section relates to Examples of sequences according to the presentinvention, including illustrative methods of selection thereof withregard to cancer; other markers were selected as described below for theindividual markers.

Description of the methodology undertaken to uncover the biomolecularsequences of the present invention

Human ESTs and cDNAs were obtained from GenBank versions 136 (Jun. 15,2003 ftp.ncbi.nih.gov/genbank/release.notes/gb136.release.notes); NCBIgenome assembly of April 2003; RefSeq sequences from June 2003; Genbankversion 139 (December 2003); Human Genome from NCBI (Build 34) (fromOctober 2003); and RefSeq sequences from December 2003. With regard toGenBank sequences, the human EST sequences from the EST (GBEST) sectionand the human mRNA sequences from the primate (GBPR1) section were used;also the human nucleotide RefSeq mRNA sequences were used (see forexample www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html and for areference to the EST section, see www.ncbi.nlm.nih.gov/dbEST/; a generalreference to dbEST, the EST database in GenBank, may be found in Boguskiet al, Nat. Genet. 1993 August; 4(4):332-3; all of which are herebyincorporated by reference as if fully set forth herein).

Novel splice variants were predicted using the LEADS clustering andassembly system as described in Sorek, R., Ast, G. & Graur, D.Alu-containing exons are alternatively spliced. Genome Res 12, 1060-7(2002); U.S. Pat. No. 6,625,545; and U.S. patent application Ser. No.10/426,002, published as US20040101876 on May 27, 2004; all of which arehereby incorporated by reference as if fully set forth herein. Briefly,the software cleans the expressed sequences from repeats, vectors andimmunoglobulins. It then aligns the expressed sequences to the genometaking alternatively splicing into account and clusters overlappingexpressed sequences into “clusters” that represent genes or partialgenes.

These were annotated using the GeneCarta (Compugen, Tel-Aviv, Israel)platform. The GeneCarta platform includes a rich pool of annotations,sequence information (particularly of spliced sequences), chromosomalinformation, alignments, and additional information such as SNPs, geneontology terms, expression profiles, functional analyses, detaileddomain structures, known and predicted proteins and detailed homologyreports.

A brief explanation is provided with regard to the method of selectingthe candidates. However, it should be noted that this explanation isprovided for descriptive purposes only, and is not intended to belimiting in any way. The potential markers were identified by acomputational process that was designed to find genes and/or theirsplice variants that are specifically expressed in cardiac tissue, asopposed to other types of tissues and also particularly as opposed tomuscle tissue, by using databases of expressed sequences. Variousparameters related to the information in the EST libraries, determinedaccording to classification by library annotation, were used to assistin locating genes and/or splice variants thereof that are specificallyand/or differentially expressed in heart tissues. The detaileddescription of the selection method and of these parameters is presentedin Example 1 below.

Selecting Candidates with Regard to Cancer

A brief explanation is provided with regard to a non-limiting method ofselecting the candidates for cancer diagnostics. However, it shouldnoted that this explanation is provided for descriptive purposes only,and is not intended to be limiting in any way. The potential markerswere identified by a computational process that was designed to findgenes and/or their splice variants that are over-expressed in tumortissues, by using databases of expressed sequences. Various parametersrelated to the information in the EST libraries, determined according toa manual classification process, were used to assist in locating genesand/or splice variants thereof that are over-expressed in canceroustissues. The detailed description of the selection method is presentedin Example 1 below. The cancer biomarkers selection engine and thefollowing wet validation stages are schematically summarized in FIG. 1.

Example 1 Identification of Differentially Expressed GeneProducts—Algorithm

In order to distinguish between differentially expressed gene productsand constitutively expressed genes (i.e., house keeping genes), analgorithm based on an analysis of frequencies was configured. A specificalgorithm for identification of transcripts specifically expressed inheart tissue is described hereinbelow.

EST Analysis

ESTs were taken from the following main sources: libraries contained inGenbank version 136 (Jun. 15, 2003ftp.ncbi.nih.gov/genbank/release.notes/gb136.release.notes) and Genbankversion 139 (December 2003); and from the LifeSeq library of IncyteCorporation (ESTs only; Wilmington, Del., USA). With regard to GenBanksequences, the human EST sequences from the EST (GBEST) section wereused.

Library annotation—EST libraries were manually classified according to:

-   -   1. Tissue origin    -   2. Biological source—Examples of frequently used biological        sources for construction of EST libraries include cancer        cell-lines; normal tissues; cancer tissues; foetal tissues; and        others such as normal cell lines and pools of normal cell-lines,        cancer cell-lines and combinations thereof. A specific        description of abbreviations used below with regard to these        tissues/cell lines etc is given above.    -   3. Protocol of library construction—various methods are known in        the art for library construction including normalized library        construction; non-normalized library construction; subtracted        libraries; ORESTES and others (described in the annotation        available in Genbank). It will be appreciated that at times the        protocol of library construction is not indicated in the        information available about that library.

The following rules were followed:

EST libraries originating from identical biological samples wereconsidered as a single library.

EST libraries which included above-average levels of contamination, suchas DNA contamination for example, were eliminated. The presence of suchcontamination was determined as follows. For each library, the number ofunspliced ESTs that are not fully contained within other splicedsequences was counted. If the percentage of such sequences (as comparedto all other sequences) was at least 4 standard deviations above theaverage for all libraries being analyzed, this library was tagged asbeing contaminated and was eliminated from further consideration in thebelow analysis (see also Sorek, R. & Safer, H. M. A novel algorithm forcomputational identification of contaminated EST libraries. NucleicAcids Res 31, 1067-74 (2003) for further details).

Clusters (genes) having at least five sequences including at least twosequences from the tissue of interest were analyzed. Splice variantswere identified by using the LEADS software package as described above

Example 2 Identification of Genes Over Expressed in Cancer

Two different scoring algorithms were developed.

Libraries score—candidate sequences which are supported by a number ofcancer libraries, are more likely to serve as specific and effectivediagnostic markers.

The basic algorithm—for each cluster the number of cancer and normallibraries contributing sequences to the cluster was counted. Fisherexact test was used to check if cancer libraries are significantlyover-represented in the cluster as compared to the total number ofcancer and normal libraries.

Library counting: Small libraries (e.g., less than 1000 sequences) wereexcluded from consideration unless they participate in the cluster. Forthis reason, the total number of libraries is actually adjusted for eachcluster.

Clones no. score—Generally, when the number of ESTs is much higher inthe cancer libraries relative to the normal libraries it might indicateactual over-expression.

The algorithm—

Clone counting: For counting EST clones each library protocol class wasgiven a weight based on an assessment of how much the protocol reflectsactual expression levels:

(i) non-normalized: 1

(ii) normalized: 0.2

(iii) all other classes: 0.1

Clones number score—The total weighted number of EST clones from cancerlibraries was compared to the EST clones from normal libraries. To avoidcases where one library contributes to the majority of the score, thecontribution of the library that gives most clones for a given clusterwas limited to 2 clones.

The score was computed as

$\frac{c + 1}{C}/\frac{n + 1}{N}$

where:

c—weighted number of “cancer” clones in the cluster.

C—weighted number of clones in all “cancer” libraries.

n—weighted number of “normal” clones in the cluster.

N—weighted number of clones in all “normal” libraries.

Clones number score significance—Fisher exact test was used to check ifEST clones from cancer libraries are significantly over-represented inthe cluster as compared to the total number of EST clones from cancerand normal libraries.

Two search approaches were used to find either general cancer-specificcandidates or tumor specific candidates.

-   -   Libraries/sequences originating from tumor tissues are counted        as well as libraries originating from cancer cell-lines        (“normal” cell-lines were ignored).    -   Only libraries/sequences originating from tumor tissues are        counted

Example 3 Identification of Tissue Specific Genes

For detection of tissue specific clusters, tissue libraries/sequenceswere compared to the total number of libraries/sequences in cluster.Similar statistical tools to those described in above were employed toidentify tissue specific genes. Tissue abbreviations are the same as forcancerous tissues, but are indicated with the header “normal tissue”.

The algorithm—for each tested tissue T and for each tested cluster thefollowing were examined:

1. Each cluster includes at least 2 libraries from the tissue T. Atleast 3 clones (weighed—as described above) from tissue T in thecluster; and

2. Clones from the tissue T are at least 40% from all the clonesparticipating in the tested cluster

Fisher exact test P-values were computed both for library and weightedclone counts to check that the counts are statistically significant.

Example 4 Identification of Splice Variants Over Expressed in Cancer ofClusters which are not Over Expressed in Cancer

Cancer-specific splice variants containing a unique region wereidentified.

Identification of unique sequence regions in splice variants

A Region is defined as a group of adjacent exons that always appear ordo not appear together in each splice variant.

A “segment” (sometimes referred also as “seg” or “node”) is defined asthe shortest contiguous transcribed region without known splicinginside.

Only reliable ESTs were considered for region and segment analysis. AnEST was defined as unreliable if:

(i) Unspliced;

(ii) Not covered by RNA;

(iii) Not covered by spliced ESTs; and

(iv) Alignment to the genome ends in proximity of long poly-A stretch orstarts in proximity of long poly-T stretch.

Only reliable regions were selected for further scoring. Unique sequenceregions were considered reliable if:

(i) Aligned to the genome; and

(ii) Regions supported by more than 2 ESTs.

The algorithm

Each unique sequence region divides the set of transcripts into 2groups:

(i) Transcripts containing this region (group TA).

(ii) Transcripts not containing this region (group TB).

The set of EST clones of every cluster is divided into 3 groups:

(i) Supporting (originating from) transcripts of group TA (S1).

(ii) Supporting transcripts of group TB (S2).

(iii) Supporting transcripts from both groups (S3).

Library and clones number scores described above were given to S1 group.

Fisher Exact Test P-values were used to check if:

S1 is significantly enriched by cancer EST clones compared to S2; and

S1 is significantly enriched by cancer EST clones compared to clusterbackground (S1+S2+S3).

Identification of unique sequence regions and division of the group oftranscripts accordingly is illustrated in FIG. 2. Each of these uniquesequence regions corresponds to a segment, also termed herein a “node”.

Region 1: common to all transcripts, thus it is not considered; Region2: specific to Transcript 1: T_(—)1 unique regions (2+6) againstT_(—)2+3 unique regions (3+4); Region 3: specific to Transcripts 2+3:T_(—)2+3 unique regions (3+4) against T1 unique regions (2+6); Region 4:specific to Transcript 3: T_(—)3 unique regions (4) against T1+2 uniqueregions (2+5+6); Region 5: specific to Transcript 1+2: T_(—)1+2 uniqueregions (2+5+6) against T3 unique regions (4); Region 6: specific toTranscript 1: same as region 2.

Example 5 Diseases and Conditions that May be Diagnosed with One or MoreVariant(s) According to the Present Invention Cardiovascular andCerebrovascular Conditions

Various examples are listed below for conditions that affect thevascular system, including various cardiovascular and cerebrovascularconditions, for which one or more variants according to the presentinvention may have a diagnostic utility. Based on these diseasesmechanisms and the correlation between the known proteins and thecardiovascular and cerebrovascular conditions, such correlation waspredicted also for one or more variants according to the presentinvention, as described below. Each variant marker of the presentinvention described herein as potential marker for cardiovascularconditions, might optionally be used alone or in combination with one ormore other variant markers described herein, and or in combination withknown markers for cardiovascular conditions, including but not limitedto Heart-type fatty acid binding protein (H-FABP), Angiotensin,C-reactive protein (CRP), myeloperoxidase (MPO), and/or in combinationwith the known protein(s) for the variant marker as described herein.Each variant marker of the present invention described herein aspotential marker for cerebrovascular conditions, might optionally beused alone or in combination with one or more other variant markersdescribed herein, and or in combination with known markers forcerebrovascular conditions, including but not limited to CRP, S100b,BNGF, CD40, MCP1, N-Acetyl-Aspartate (NAA), N-methyl-d-aspartate (NMDA)receptor antibodies (NR2Ab), and/or in combination with the knownprotein(s) for the variant marker as described herein.

Myocardial Infarction

HSFLT variants, HSI1Ra variants, HSPLGF variants, HUMSP18A variants,F05068 variants and/or HUMIL10 variants are potential markers formyocardial infarction. Other conditions that may be diagnosed by thesemarkers or variants of them include but are not limited to the presence,risk and/or extent of the following:

-   1. Myocarditis—in myocarditis cardiac muscle cells can go through    cell lysis and leakage with the release of intracellular content to    the extracellular space and blood, a similar process as happens in    myocardial infarction (see also extended description below).-   2. Angina—stable or unstable, as the reduction of oxygen delivery to    part of the heart often leads to local ischemic conditions that    facilitate leakage of intracellular content.-   3. Traumatic injury to myocardial tissue—blunt or penetrating, may    also result in myocardial cell leakage.-   4. Opening an occluded coronary artery following thrombolytic    therapy—If such treatment is successful, proteins and other products    of the local tissue are washed into the blood and can be detected    there.-   5. Cardiomyopathy—which is characterized by slow degeneration of the    heart muscle (see also extended description below).-   6. Myocardial injury after rejection of heart transplant.-   7. Congestive heart failure where heart myocytes slowly degenerate    (as had been shown for Troponin-I; see also extended description    below).-   8. Future cardiovascular disease (as a risk factor).-   9. Conditions which have similar clinical symptoms as myocardial    infarction and where the differential diagnosis between them and    myocardial infarction is of clinical importance including but not    limited to:    -   a. Clinical symptoms resulting from lung related tissue (e.g.        Pleuritis, pulmonary embolism)    -   b. Musculoskeletal origin of pain    -   c. Clinical symptoms resulting from heart related tissue which        are not due to myocardial infarction, e.g. acute pericarditis    -   d. Upper abdominal pain from abdominal organs including but nor        limited to esophagitis, gastro-esophageal reflux, gastritis,        gastric ulcer, duodenitis, duodenal ulcer, enteritis,        gastroenteritis, cholecystitis, cholelithiasis,        cholangiolithiasis, pancreatitis, splenic infarction, splenic        trauma, Aortic dissection.

One or more of these markers (variants according to the presentinvention) may optionally be used a tool to decide on treatment optionse.g. anti platelet inhibitors (as has been shown for Troponin-I); as atool in the assessment of pericardial effusion; and/or as a tool in theassessment of endocarditis and/or rheumatic fever, where progressivedamage to the heart muscle may occur.

Acute and Chronic Inflammation and Risk Factors for CVS Diseases

HSFLT variants, HSI1Ra variants, HSPLGF variants, HUMSP18A variants,F05068 variants and/or HUMIL10 variants are potential markers forinflammation, including a spectrum of diseases where an inflammatoryprocess plays a substantial role. In addition CRP levels and inparticular baseline levels serve as a risk factor for various diseases,particularly cardiovascular diseases where inflammation is thought toparticipate in the pathogenesis. Conditions that may be diagnosed bythese markers or variants of them include but are not limited to thepresence, risk and/or extent of the following:

-   1. Conditions that entail an inflammatory process that involves    blood vessels including but not limited to hypercholesterolemia,    diabetes, atherosclerosis, inflammation that involves blood    vessels—whether acute or chronic including but not limited to the    coronary arteries and blood vessels of the brain, myocardial    infarction, cerebral stroke, peripheral vascular disease,    vasculitis, polyarteritis nodosa, ANCA associated small vessel    vasculitis, Churg-Strauss syndrome, Henoch-Schonlein purpura,    scleroderma, thromboangiitis obliterans, temporal arteritis,    Takayasu's arteritis, hypersensitivity vasculitis, Kawasaki disease,    Behçet syndrome, and their complications including but not limited    to coronary disease, angina pectoris, deep vein thrombosis, renal    disease, diabetic nephropathy, lupus nephritis, renal artery    thrombosis, renal artery stenosis, atheroembolic disease of the    renal arteries, renal vein thrombosis, hemolytic uremic syndrome,    thrombotic thrombocytopenic purpura, arteriolar nephrosclerosis,    preeclampsia, eclampsia, albuminuria, microalbuminuria,    glomerulonephritis, renal failure, hypertension, uremia,    cerebrovascular disease, peripheral vascular disease, intermittent    claudication, abdominal angina.-   2. Rheumatic/autoimmune diseases that involve systemic immune    reaction including but not limited to rheumatoid arthritis,    scleroderma, mixed connective tissue disease, Sjogren syndrome,    ankylosing spondylitis, spondyloarthropathy, psoriasis, psoriatic    arthritis, myositis and systemic lupus erythematosus.-   3. Acute and/or chronic infective processes that involve systemic    immune reaction including but not limited to pneumonia, bacteremia,    sepsis, pyelonephritis, cellulitis, osteomyelitis, meningitis and    viral hepatitis.-   4. Malignant and idiopathic processes that involve systemic immune    reaction and/or proliferation of immune cells including but not    limited to granulomatous disorders, Wegener's granulomatosis,    lymphomatoid granulomatosis/polymorphic reticulosis, idiopathic    midline granuloma, multiple myeloma, Waldenstrom's    macroglobulinemia, Castleman's disease, amyloidosis, lymphoma,    histiocytosis, renal cell carcinoma and paraneoplastic syndromes.-   5. Conditions where CRP was shown to have a positive correlation    with the presence of the condition including but not limited to    weight loss, anorexia-cachexia syndrome, extent of disease,    recurrence in advanced cancer, diabetes (types 1 & 2), obesity,    hypertension, preterm delivery.-   6. Conditions which have similar symptoms, signs and complications    as the conditions above and where the differential diagnosis between    them and the conditions above is of clinical importance including    but not limited to:    -   a. Other (non vascular) causes of heart disease, renal disease        and cerebral disease.    -   b. Other (non rheumatic) causes of arthropathy and        musculoskeletal pain.    -   c. Other causes of non-specific symptoms and signs such as fever        of unknown origin, loss of appetite, weight loss, nonspecific        pains, breathing difficulties and anxiety.

Stroke

Stroke is a manifestation of vascular injury to the brain which iscommonly secondary to atherosclerosis or hypertension, and is the thirdleading cause of death (and the second most common cause of neurologicdisability) in the United States. Embodiments of marker(s) for diagnosisof stroke and related conditions as described herein may optionally beselected from the group consisting of HSFLT variants, HSI1Ra variants,HSPLGF variants, HUMSP18A variants, F05068 variants and/or HUMIL10variants or markers related thereto.

Specific markers of neural tissue injury are found in the blood or inblood components such as serum and plasma, as well as the CSF of apatient experiencing stroke or TIAs. Furthermore, clearance of theobstructing object in ischemic stroke can cause injury from oxidativeinsult during reperfusion, and patients with ischemic stroke cansometimes experience hemorrhagic transformation as a result ofreperfusion or thrombolytic therapy.

Fibrinolysis is the process of proteolytic clot dissolution. In a manneranalogous to coagulation, fibrinolysis is mediated by serine proteinasesthat are activated from their zymogen form. The serine proteinaseplasmin is responsible for the degradation of fibrin into smallerdegradation products that are liberated from the clot, resulting in clotdissolution. Fibrinolysis is activated soon after coagulation in orderto regulate clot formation. Endogenous serine proteinase inhibitors alsofunction as regulators of fibrinolysis.

The presence of a coagulation or fibrinolysis marker in cerebrospinalfluid would indicate that activation of coagulation or fibrinolysis,depending upon the marker used, coupled with increased permeability ofthe blood-brain barrier has occurred. In this regard, more definitiveconclusions regarding the presence of coagulation or fibrinolysismarkers associated with acute stroke may be obtained using cerebrospinalfluid.

Stroke can be categorized into two broad types, “ischemic stroke” and“hemorrhagic stroke.” Additionally, a patient may experience transientischemic attacks, which are in turn a high risk factor for the futuredevelopment of a more severe episode.

Ischemic stroke encompasses thrombotic, embolic, lacunar andhypoperfusion types of strokes. Thrombi are occlusions of arteriescreated in situ within the brain, while emboli are occlusions caused bymaterial from a distant source, such as the heart and major vessels,often dislodged due to myocardial infarct or atrial fibrillation. Lessfrequently, thrombi may also result from vascular inflammation due todisorders such as meningitis. Thrombi or emboli can result fromatherosclerosis or other disorders, for example, arteritis, and lead tophysical obstruction of arterial blood supply to the brain. Lacunarstroke refers to an infarct within non-cortical regions of the brain.Hypoperfusion embodies diffuse injury caused by non-localized cerebralischemia, typically caused by myocardial infarction and arrhythmia.

The onset of ischemic stroke is often abrupt, and can become an“evolving stroke” manifested by neurologic deficits that worsen over a24-48 hour period. In evolving stroke, “stroke-associated symptom(s)”commonly include unilateral neurologic dysfunction which extendsprogressively, without producing headache or fever. Evolving stroke mayalso become a “completed stroke,” in which symptoms develop rapidly andare maximal within a few minutes.

Hemorrhagic stroke is caused by intracerebral or subarachnoidhemorrhage, i.e., bleeding into brain tissue, following blood vesselrupture within the brain. Intracerebral and subarachnoid hemorrhage aresubsets of a broader category of hemorrhage referred to as intracranialhemorrhage. Intracerebral hemorrhage is typically due to chronichypertension, and a resulting rupture of an arteriosclerotic vessel.Stroke-associated symptom(s) of intracerebral hemorrhage are abrupt,with the onset of headache and steadily increasing neurologicaldeficits. Nausea, vomiting, delirium, seizures and loss of consciousnessare additional common stroke-associated symptoms.

In contrast, most subarachnoid hemorrhage is caused by head trauma oraneurysm rupture which is accompanied by high pressure blood releasewhich also causes direct cellular trauma. Prior to rupture, aneurysmsmay be asymptomatic, or occasionally associated with tension or migraineheadaches. However, headache typically becomes acute and severe uponrupture, and may be accompanied by varying degrees of neurologicaldeficit, vomiting, dizziness, and altered pulse and respiratory rates.

Transient ischemic attacks (TIAs) have a sudden onset and briefduration, typically 2-30 minutes. Most TIAs are due to emboli fromatherosclerotic plaques, often originating in the arteries of the neck,and can result from brief interruptions of blood flow. The symptoms ofTIAs are identical to those of stroke, but are only transient.Concomitant with underlying risk factors, patients experiencing TIAs areat a markedly increased risk for stroke.

Current diagnostic methods for stroke include costly and time-consumingprocedures such as noncontrast computed tomography (CT) scan,electrocardiogram, magnetic resonance imaging (MRI), and angiography.Determining the immediate cause of stroke and differentiating ischemicfrom hemorrhagic stroke is difficult. CT scans can detect parenchymalbleeding greater than 1 cm and 95% of all subarachnoid hemorrhages. CTscan often cannot detect ischemic strokes until 6 hours from onset,depending on the infarct size. MRI may be more effective than CT scan inearly detection of ischemic stroke, but it is less accurate atdifferentiating ischemic from hemorrhagic stroke, and is not widelyavailable. An electrocardiogram (ECG) can be used in certaincircumstances to identify a cardiac cause of stroke. Angiography is adefinitive test to identify stenosis or occlusion of large and smallcranial blood vessels, and can locate the cause of subarachnoidhemorrhages, define aneurysms, and detect cerebral vasospasm. It is,however, an invasive procedure that is also limited by cost andavailability. Coagulation studies can also be used to rule out acoagulation disorder (coagulopathy) as a cause of hemorrhagic stroke.

Immediate diagnosis and care of a patient experiencing stroke can becritical. For example, tissue plasminogen activator (TPA) given withinthree hours of symptom onset in ischemic stroke is beneficial forselected acute stroke patients. Alternatively, patients may benefit fromanticoagulants (e.g., heparin) if they are not candidates for TPAtherapy. In contrast, thrombolytics and anticoagulants are stronglycontraindicated in hemorrhagic strokes. Thus, early differentiation ofischemic events from hemorrhagic events is imperative. Moreover, delaysin the confirmation of stroke diagnosis and the identification of stroketype limit the number of patients that may benefit from earlyintervention therapy. Finally, there are currently no diagnostic methodsthat can identify a TIA, or predict delayed neurological deficits whichare often detected at a time after onset concurrent with thepresentation of symptoms.

Accordingly, there is a present need in the art for a rapid, sensitiveand specific diagnostic assay for stroke and TIA that can alsodifferentiate the stroke type and identify those individuals at risk fordelayed neurological deficits. Such a diagnostic assay would greatlyincrease the number of patients that can receive beneficial stroketreatment and therapy, and reduce the costs associated with incorrectstroke diagnosis.

The present invention relates to the identification and use ofdiagnostic markers for stroke and neural tissue injury. The methods andcompositions described herein can meet the need in the art for rapid,sensitive and specific diagnostic assay to be used in the diagnosis anddifferentiation of various forms of stroke and TIAs. Moreover, themethods and compositions of the present invention can also be used tofacilitate the treatment of stroke patients and the development ofadditional diagnostic and/or prognostic indicators.

In various aspects, the invention relates to materials and proceduresfor identifying markers that are associated with the diagnosis,prognosis, or differentiation of stroke and/or TIA in a patient; tousing such markers in diagnosing and treating a patient and/or tomonitor the course of a treatment regimen; to using such markers toidentify subjects at risk for one or more adverse outcomes related tostroke and/or TIA; and for screening compounds and pharmaceuticalcompositions that might provide a benefit in treating or preventing suchconditions.

In a first aspect, the invention discloses methods for determining adiagnosis or prognosis related to stroke, or for differentiating betweentypes of strokes and/or TIA. These methods comprise analyzing a testsample obtained from a subject for the presence or amount of one or moremarkers for neural tissue injury. These methods can comprise identifyingone or more markers, the presence or amount of which is associated withthe diagnosis, prognosis, or differentiation of stroke and/or TIA. Oncesuch marker(s) are identified, the level of such marker(s) in a sampleobtained from a subject of interest can be measured. In certainembodiments, these markers can be compared to a level that is associatedwith the diagnosis, prognosis, or differentiation of stroke and/or TIA.By correlating the subject's marker level(s) to the diagnostic markerlevel(s), the presence or absence of stroke, the probability of futureadverse outcomes, etc., in a patient may be rapidly and accuratelydetermined.

In a related aspect, the invention discloses methods for determining thepresence or absence of a disease in a subject that is exhibiting aperceptible change in one or more physical characteristics (that is, oneor more “symptoms”) that are indicative of a plurality of possibleetiologies underlying the observed symptom(s), one of which is stroke.These methods comprise analyzing a test sample obtained from the subjectfor the presence or amount of one or more markers selected to rule in orout stroke, or one or more types of stroke, as a possible etiology ofthe observed symptom(s). Etiologies other than stroke that are withinthe differential diagnosis of the symptom(s) observed are referred toherein as “stroke mimics”, and marker(s) able to differentiate one ormore types of stroke from stroke mimics are referred to herein as“stroke differential diagnostic markers”. The presence or amount of suchmarker(s) in a sample obtained from the subject can be used to rule inor rule out one or more of the following: stroke, thrombotic stroke,embolic stroke, lacunar stroke, hypoperfusion, intracerebral hemorrhage,and subarachnoid hemorrhage, thereby either providing a diagnosis(rule-in) and/or excluding a diagnosis (rule-out).

Obtaining information on the true time of onset can be critical, asearly treatments have been reported to be critical for proper treatment.Obtaining this time-of-onset information may be difficult, and is oftenbased upon interviews with companions of the stroke victim. Thus, invarious embodiments, markers and marker panels are selected todistinguish the approximate time since stroke onset. For purposes of thepresent invention, the term “acute stroke” refers to a stroke that hasoccurred within the prior 12 hours, more preferably within the prior 6hours, and most preferably within the prior 3 hours; while the term“non-acute stroke” refers to a stroke that has occurred more than 12hours ago, preferably between 12 and 48 hours ago, and most preferablybetween 12 and 24 hours ago. Embodiments of markers for differentiatingbetween acute and non-acute strokes, referred to herein as stroke “timeof onset markers” are described hereinafter.

For markers appearing in the patent which are already linked to stroke,either ischemic or hemorrhagic, variants could also help to diagnose,directly or by elimination of other conditions including but not limitedto:

1. Transient ischemic attack2. Brain trauma, in case it is unclear whether accompanied by stroke ornot

3. Migraine

4. Bleeding in any part of the brain or inside the skull that cause ordidn't cause damage to brain tissue

5. Tumor

In addition, such markers may help determine:1. The time of stroke2. The type of stroke3. The extent of tissue damage as a result of the stroke4. Response to immediate treatments that are meant to alleviate theextent of stroke and brain damage, when available.

With regard to stroke, according to embodiments of the presentinvention, the panel may optionally and preferably provide diagnosis ofstroke and indication if an ischemic stroke has occurred; diagnosis ofstroke and indication if a hemorrhagic stroke has occurred; diagnosis ofstroke, indication if an ischemic stroke has occurred, and indication ifa hemorrhagic stroke has occurred; diagnosis of stroke and prognosis ofa subsequent cerebral vasospasm; and diagnosis of stroke, indication ifa hemorrhagic stroke has occurred, and prognosis of a subsequentcerebral vasospasm.

According to other optional embodiments of the present invention, thereare provided methods of identifying a patient at risk for cerebralvasospasm. Such methods preferably comprise comparing an amount of oneor more marker(s) predictive of a subsequent cerebral vasospasm in atest sample from a patient diagnosed with a subarachnoid hemorrhage.Such markers may be one or more markers related to blood pressureregulation, markers related to inflammation, markers related toapoptosis, and/or specific markers of neural tissue injury. As discussedherein, such marker may be used in panels comprising 2, 3, 4, 5, 6, 7,8, 9, 10, 15, 20, or more or individual markers. Embodiments ofmarker(s) may be selected from the group consisting of HSFLT variants,HSI1Ra variants, HSPLGF variants, HUMSP18A variants, F05068 variantsand/or HUMIL10 variants or markers related thereto. The levels of one ormore markers may be compared to a predictive level of said marker(s),wherein said patient is identified as being at risk for cerebralvasospasm by a level of said marker(s) equal to or greater than saidpredictive level. In the alternative, a panel response value for aplurality of such markers may be determined, optionally considering achange in the level of one or more such markers as an additionalindependent marker.

According to yet other embodiments of the present invention, there areprovided methods of differentiating ischemic stroke from hemorrhagicstroke using such marker panels.

Cardiomyopathy and Myocarditis

Cardiomyopathy may be treated with the polynucleotides/polypeptidesand/or methods of this invention. Cardiomyopathy is a general diagnosticterm designating primary myocardial disease which may progress to heartfailure. The disease comprises inflammatory cardiomyopathies,cardiomyopathies resulting from a metabolic disorder such as anutritional deficiency or by altered endocrine function, exposure totoxic substances, for example from alcohol or exposure to cobalt orlead, infiltration and deposition of abnormal. In some embodiments, themarker(s) for diagnosis of cardiomyopathy and myocarditis, and relatedconditions as described herein, may optionally be selected from thegroup consisting of HSFLT variants, HSI1Ra variants, HSPLGF variants,HUMSP18A variants, F05068 variants and/or HUMIL10 variants

Congestive Heart Failure (CHF)

HSFLT variants, HSI1Ra variants, HSPLGF variants, HUMSP18A variants,F05068 variants and/or HUMIL10 variants are potential markers for, andmay be used to treat, etc., CHF.

The invention provides a means for the identification/prognostication,etc., of a number of conditions including the assessment of thepresence, risk and/or extent of the following:

-   1. A risk factor for sudden cardiac death, from arrhythmia or any    other heart related reason.-   2. Rejection of a transplanted heart.-   3. Conditions that lead to heart failure including but not limited    to myocardial infarction, angina, arrhythmias, valvular diseases,    atrial and/or ventricular septal defects.-   4. Conditions that cause atrial and or ventricular wall volume    overload. Wall stretch results in enhanced secretion of cardiac    extracellular regulators. Such conditions include but are not    limited to systemic arterial hypertension, pulmonary hypertension    and pulmonary embolism.-   5. Conditions which have similar clinical symptoms as heart failure    and as states that cause atrial and or ventricular    pressure-overload, where the differential diagnosis between these    conditions to the latter is of clinical importance including but not    limited to breathing difficulty and/or hypoxia due to pulmonary    disease, anemia or anxiety.

Cancerous Conditions

Various non-limiting examples are given below of cancerous conditionsfor which one or more variants according to the present invention mayhave a diagnostic, or therapeutic utility.

Ovarian Cancer

Ovarian cancer causes more deaths than any other cancer of the femalereproductive system, however, only 25% of ovarian cancers are detectedin stage I. No single marker has been shown to be sufficiently sensitiveor specific to contribute to the diagnosis of ovarian cancer.

In one embodiment, the markers of this invention are utilized alone, orin combination with other markers, for the diagnosis, treatment orassessment of prognosis of ovarian cancer. Such other markers maycomprise CA-125 or mucin 16, CA-50, CA 54-61, CA-195 and CA 19-9, STNand TAG-72, kallikreins, cathepsin L, urine gonadotropin, inhibins,cytokeratins, such as TPA and TPS, members of the Transforming GrowthFactors (TGF) beta superfamily, Epidermal Growth Factor, p53 and HER-2or any combination thereof.

Immunohistochemistry may be used to assess the origin of the tumor andstaging as part of the methods of this invention, and as protected usesfor the polypeptides of this invention.

In some embodiments, this invention providespolypeptides/polynucleotides which serves as markers for ovarian cancer.In some embodiments, the marker is any polypeptide/polynucleotide asdescribed herein. In some embodiments, the marker is an HSFLT, Z25299 orvariants as described herein or markers related thereto. Each variantmarker of the present invention described herein may be used alone or incombination with one or more other variant ovarian cancer describedherein, and/or in combination with known markers for ovarian cancer, asdescribed herein. Diagnosis of ovarian cancer and or of other conditionsthat may be diagnosed by these markers or variants of them include butare not limited to the presence, risk and/or extent of the following:

-   -   1. The identification of a metastasis of unknown origin which        originated from a primary ovarian cancer, for example gastric        carcinoma (such as Krukenberg tumor), breast cancer, colorectal        carcinoma and pancreatic carcinoma.    -   2. As a marker to distinguish between different types of ovarian        cancer, therefore potentially affect treatment choice (e.g.        discrimination between epithelial tumors and germ cell tumors).    -   3. As a tool in the assessment of abdominal mass and in        particular in the differential diagnosis between a benign and        malignant ovarian cysts.    -   4. As a tool for the assessment of infertility.    -   5. Other conditions that may elevate serum levels of ovary        related markers. These include but are not limited to: cancers        of the endometrium, cervix, fallopian tubes, pancreas, breast,        lung and colon; nonmalignant conditions such as pregnancy,        endometriosis, pelvic inflammatory disease and uterine fibroids.    -   6. Conditions which have similar symptoms, signs and        complications as ovarian cancer and where the differential        diagnosis between them and ovarian cancer is of clinical        importance including but not limited to:        -   a. Non-malignant causes of pelvic mass. Including, but not            limited to: benign (functional) ovarian cyst, uterine            fibroids, endometriosis, benign ovarian neoplasms and            inflammatory bowel lesions        -   b. Any condition suggestive of a malignant tumor including            but not limited to anorexia, cachexia, weight loss, fever,            hypercalcemia, skeletal or abdominal pain, paraneoplastic            syndrome.        -   c. Ascites.    -   7. Prediction of patient's drug response    -   8. As surrogate markers for clinical outcome of a treated        cancer.

Breast Cancer

Breast cancer is the most commonly occurring cancer in women, comprisingalmost a third of all malignancies in females. In one embodiment, thepolypeptides and/or polynucleotides of this invention are utilizedalone, or in combination with other markers, for the diagnosis,treatment or assessment of prognosis of breast cancer. In oneembodiment, the polypeptides and/or polynucleotides serve as markers ofdisease.

Such markers may be used alone, or in combination with other knownmarkers for breast cancer, including, inter alia, Mucin1 (measured as CA15-3), CEA (CarcinoEmbryonic Antigen), HER-2, CA125, CA 19-9, PCNA,Ki-67, E-Cadherin, Cathepsin D, TFF1, epidermal growth factor receptor(EGFR), cyclin E, p53, bcl-2, vascular endothelial growth factor,urokinase-type plasminogen activator-1, survivin, or any combinationthereof, and includes use of any compound which detects or quantifiesthe same. ESR (Erythrocyte Sedimentation Rate) values may be obtained,and comprise the marker panel for breast cancer.

In some embodiments, the polypeptides/polynucleotides of this inventionserve as prognosticators, in identifying, inter alia, patients atminimal risk of relapse, patients with a worse prognosis, or patientslikely to benefit from specific treatments.

There are some non-cancerous pathological conditions which represent anincreased risk factor for development breast cancer, and as such,patients with these conditions may be evaluated using thepolypeptides/polynucleotides and according to the methods of thisinvention, for example, as part of the screening methods of thisinvention, Some of these conditions include, but are not limited toductal hyperplasia without atypia, atypical hyperplasia, and others.

In some embodiments, the polypeptides/polynucleotides of this inventionserve as markers for breast cancer, including, but not limited to:HSFLT, AA336074, Z25299 or homologues thereof. In some embodiments, theHSFLT, AA336074, Z25299 or polynucleotides encoding the same, can beused alone or in combination with any other desired marker, including,inter alia, Calcitonin, CA15-3 (Mucin1), CA27-29, TPA, a combination ofCA 15-3 and CEA, CA 27.29 (monoclonal antibody directed against MUC1),Estrogen 2 (beta), HER-2 (c-erbB2), or any combinations thereof.

In some embodiments, the polypeptides/polynucleotides of this inventionmay be useful in, inter alia, assessing the presence, risk and/or extentof the following:

-   1. The identification of a metastasis of unknown origin which    originated from a primary breast cancer tumor.-   2. In the assessment of lymphadenopathy, and in particular axillary    lymphadenopathy.-   3. As a marker to distinguish between different types of breast    cancer, therefore potentially affect treatment choice (e.g. as    HER-2)-   4. As a tool in the assessment of palpable breast mass and in    particular in the differential diagnosis between a benign and    malignant breast mass.-   5. As a tool in the assessment of conditions affecting breast skin    (e.g. Paget's disease) and their differentiation from breast cancer.-   6. As a tool in the assessment of breast pain or discomfort    resulting from either breast cancer or other possible conditions    (e.g. Mastitis, Mondors syndrome).-   7. Other conditions not mentioned above which have similar symptoms,    signs and complications as breast cancer and where the differential    diagnosis between them and breast cancer is of clinical importance    including but not limited to:    -   a. Abnormal mammogram and/or nipple retraction and/or nipple        discharge due to causes other than breast cancer. Such causes        include but are not limited to benign breast masses, melanoma,        trauma and technical and/or anatomical variations.    -   b. Any condition suggestive of a malignant tumor including but        not limited to anorexia, cachexia, weight loss, fever,        hypercalcemia, paraneoplastic syndrome.

Lymphadenopathy, weight loss and other signs and symptoms associatedwith breast cancer but originate from diseases different from breastcancer including but not limited to other malignancies, infections andautoimmune diseases.

-   8. Prediction of patient's drug response-   9. As surrogate markers for clinical outcome of a treated cancer.

Lung Cancer

Lung cancer is the primary cause of cancer death among both men andwomen in the U.S. In one embodiment, the polypeptides and/orpolynucleotides of this invention are utilized alone, or in combinationwith other markers, for the diagnosis, treatment or assessment ofprognosis of lung cancer. In one embodiment, the term “lung cancer” isto be understood as encompassing small cell or non-small cell lungcancers, including adenocarcinomas, bronchoalveolar-alveolar, squamouscell and large cell carcinomas.

In some embodiments, the polypeptides/polynucleotides of this inventionare utilized in conjunction with other screening procedures, as well asthe use of other markers, for the diagnosis, or assessment of prognosisof lung cancer in a subject. In some embodiments, such screeningprocedures may comprise the use of chest x-rays, analysis of the type ofcells contained in sputum, fiberoptic examination of the bronchialpassages, or any combination thereof. Such evaluation in turn may impactthe type of treatment regimen pursued, which in turn may reflect thetype and stage of the cancer, and include surgery, radiation therapyand/or chemotherapy.

Current radiotherapeutic agents, chemotherapeutic agents and biologicaltoxins are potent cytotoxins, yet do not discriminate between normal andmalignant cells, producing adverse effects and dose-limiting toxicities.In some embodiments of this invention, the polypeptides/polynucleotidesprovide a means for more specific targeting to neoplastic versus normalcells.

In some embodiments, the polypeptides for use in the diagnosis,treatment and/or assessment of progression of lung cancer may comprise:HSFLT, HSI1RA, HSPLGF, HUMSP18A, F05068, Z25299, AA336074 or homologousthereof, or polynucleotides encoding the same. In some embodiments,these polypeptides/polynucleotides may be used alone or in combinationwith one or more other appropriate markers, including, inter alia, otherpolypeptides/polynucleotides of this invention. In some embodiments,such use may be in combination with other known markers for lung cancer,including but not limited to CEA, CA15-3, Beta-2-microglobulin, CA19-9,TPA, and/or in combination with native sequences associated with thepolypeptides/polynucleotides of this invention, as herein described.

In some embodiments, the polypeptides/polynucleotides of this inventionmay be useful in, inter alia, assessing the presence, risk and/or extentof the following:

-   1. The identification of a metastasis of unknown origin which    originated from a primary lung cancer.-   2. The assessment of a malignant tissue residing in the lung that is    from a non-lung origin, including but not limited to: osteogenic and    soft tissue sarcomas; colorectal, uterine, cervix and corpus tumors;    head and neck, breast, testis and salivary gland cancers; melanoma;    and bladder and kidney tumors.-   3. Distinguishing between different types of lung cancer, therefore    potentially affect treatment choice (e.g. small cell vs. non small    cell tumors).-   4. Unexplained dyspnea and/or chronic cough and/or hemoptysis, and    analysis thereof.-   5. Differential diagnosis of the origin of a pleural effusion.-   6. Conditions which have similar symptoms, signs and complications    as lung cancer and where the differential diagnosis between them and    lung cancer is of clinical importance including but not limited to:    -   a. Non-malignant causes of lung symptoms and signs. Symptoms and        signs include, but are not limited to: lung lesions and        infiltrates, wheeze, stridor.    -   b. Other symptoms, signs and complications suggestive of lung        cancer, such as tracheal obstruction, esophageal compression,        dysphagia, recurrent laryngeal nerve paralysis, hoarseness,        phrenic nerve paralysis with elevation of the hemidiaphragm and        Horner syndrome.    -   c. Any condition suggestive of a malignant tumor including but        not limited to anorexia, cachexia, weight loss, fever,        hypercalcemia, hypophosphatemia, hyponatremia, syndrome of        inappropriate secretion of antidiuretic hormone, elevated ANP,        elevated ACTH, hypokalemia, clubbing, neurologic-myopathic        syndromes and thrombophlebitis.-   7. Prediction of patient's drug response-   8. As surrogate markers for clinical outcome of a treated cancer.

Colorectal Cancer:

Colon and rectal cancers are malignant conditions which occur in thecorresponding segments of the large intestine. In one embodiment, thepolypeptides and/or polynucleotides of this invention are utilizedalone, or in combination with other markers, for the diagnosis,treatment or assessment of prognosis of colorectal cancer. In someembodiments, the term “colorectal cancers” is to be understood asencompassing adenocarcinomas, carcinoid tumors, for example, found inthe appendix and rectum; gastrointestinal stromal tumors for example,found in connective tissue in the wall of the colon and rectum; andlymphomas, which are malignancies of immune cells in the colon, rectumand lymph nodes. In some embodiments, the polypeptides/polynucleotidesare useful in diagnosing, treating and/or assessing progression ofcolorectal pathogenesis, including the maturation of adenomatous polyps,to larger polyps, and all relevant stages in the neoplastictransformation of the tissue.

In some embodiments, the polypeptides/polynucleotides of this inventionare utilized in conjunction with other screening procedures, as well asthe use of other markers, for the diagnosis, or assessment of prognosisof colorectal cancer in a subject. In some embodiments, such screeningprocedures may comprise fecal occult blood tests, sigmoidoscopy, bariumenema X-ray, digital rectal exam, colonoscopy, detection ofcarcinoembryonic antigen (CEA) or combinations thereof.

In some embodiments, the polypeptides/polynucleotides are useful inassessing progression of colorectal pathogenesis. Such assessment mayreflect the staging of the colorectal cancer. In some embodiments, thepolypeptides/polynucleotides are useful in assessing or altering stageprogression in a subject with colorectal cancer. When in reference tocancer staging, it is to be understood that any known means orclassification system will apply, for any embodiment as describedherein. In some embodiments, staging in reference to colorectal cancermay be via the Dukes' system and/or the International Union againstCancer-American Joint Committee on Cancer TNM staging system. Stagingwill reflect, in some embodiments, the extent of tumor penetration intothe colon wall, with greater penetration generally correlating with amore dangerous tumor; the extent of invasion of the tumor through thecolon wall and into other neighboring tissues, with greater invasiongenerally correlating with a more dangerous tumor; the extent ofinvasion of the tumor into the regional lymph nodes, and the extent ofmetastatic invasion into more distant tissues, such as the liver. It isto be understood that the polypeptides/polynucleotides of this inventionmay be useful both in the identification/assessment of colorectal cancerpathogenesis as a function of stage designation, as well as

In some embodiments, the polypeptides/polynucleotides of this inventionmay be useful in the diagnosis, treatment and/or assessment of prognosisof colon cancer. According to this aspect and in one embodiment, thepolypeptides useful in this context are: HSFLT, HSPLGF, Z25299 orhomologues thereof, or polynucleotides encoding the same. In someembodiments, these polypeptides/polynucleotides are used alone or incombination with one or more other polypeptides/polynucleotides of thisinvention, and/or in combination with other markers for colorectalcancer, including but not limited to CEA, CA19-9, CA50, and/or incombination with a native protein associated with the polypeptides ofthis invention, for example, native proteins of which the polypeptidesare variants thereof. In some embodiments, thepolypeptides/polynucleotides of this invention may be useful in, interalia, assessing the presence, risk and/or extent of the following:

-   1. Early diagnosis, staging, grading, prognosis, monitoring, and    treatment of diseases associated with colon cancer, or to indicate a    predisposition to such for preventative measures.-   2. The identification of a metastasis of unknown origin which    originated from a primary colorectal cancer tumor, in particular    when the metastasis is located in the liver, lung, bones,    supraclavicluar lymph nodes or brain.-   3. In the assessment of lymphadenopathy, in particular    supraclavicluar or internal abdominal lymphadenopathy.-   4. As a marker to distinguish between different types of colorectal    tumors including but not limited to nonhereditary carcinoma,    Familial Polyposis Coli, Hereditary nonpolyposis colon cancer (Lynch    syndrome) and Carcinoid; therefore potentially affect treatment    choice.-   5. In the assessment of cancer staging, in addition and as a    complementary measure to the Dukes system for staging colorectal    cancer.-   6. As a risk factor to the development of colorectal tumor, and in    particular in diseases known to have high incidence of colorectal    tumor, including but not limited to Crohn's disease and Ulcerative    Colitis.-   7. As a tool in the assessment of fecal occult blood or imaging    findings suspected for colorectal tumor or abnormal blood tests    associated with colorectal cancer including but not limited to    elevated CEA level.-   8. In the differential diagnosis between malignant and benign    colorectal tumors, in particular adenomas and polyps.-   9. Other conditions not mentioned above which have similar symptoms,    signs and complications as colorectal cancer and where the    differential diagnosis between them and colorectal cancer is of    clinical importance including but not limited to:    -   a. Any condition suggestive of a malignant tumor including but        not limited to anorexia, cachexia, weight loss, fever,        hypercalcemia, paraneoplastic syndrome.    -   b. Lymphadenopathy, weight loss and other signs and symptoms        associated with colorectal cancer but originate from diseases        different from colorectal cancer including but not limited to        other malignancies, infections and autoimmune diseases.-   10. Prediction of patient's drug response-   11. As surrogate markers for clinical outcome of a treated cancer.

Prostate Cancer

Prostate cancer is the most commonly diagnosed malignancy and the secondmost frequent cause of cancer-related deaths in the western malepopulation. In one embodiment, the polypeptides and/or polynucleotidesof this invention are utilized alone, or in combination with othermarkers, for the diagnosis, treatment or assessment of prognosis ofprostate cancer.

In some embodiments, the polypeptides/polynucleotides of this inventionare utilized in conjunction with other screening procedures, as well asthe use of other markers, for the diagnosis, or assessment of prognosisof colorectal cancer in a subject. In some embodiments, such markers maycomprise prostatic acid phosphatase (PAP), prostate-specific antigen(PSA), prostate-specific membrane antigen (PSM), PCA3 DD3 orcombinations thereof.

In some embodiments, the polypeptides/polynucleotides of this inventionmay be useful in the diagnosis, treatment and/or assessment of prognosisof prostate cancer. According to this aspect and in one embodiment, thepolypeptides useful in this context are: AA336074, Z22012, HUMTREFAC,homologues thereof, or polynucleotides encoding the same. In someembodiments, these polypeptides/polynucleotides are used alone or incombination with one or more other polypeptides/polynucleotides of thisinvention, and/or in combination with other markers, including, interalia, PSA, PAP (prostatic acid phosphatase), CPK-BB, PSMA, PCA3, DD3,and/or a native protein associated with the polypeptides of thisinvention, for example, native proteins of which the polypeptides arevariants thereof. In some embodiments the polypeptides/polynucleotidesof this invention are useful in the diagnosis of prostate cancer, whichincludes, inter alia, the differential diagnosis between prostate cancerand BPH, prostatitis and/or prostatism.

Candidate Markers

The markers of the present invention were tested with regard to theirexpression in various tissue samples. Unless otherwise noted, allexperimental data relates to variants of the present invention, namedaccording to the segment being tested (as expression was tested throughRT-PCR as described). A description of the samples used in the ovariancancer testing panel is provided in Table 1 below. A description of thesamples used in the colon cancer testing panel is provided in Table 2below. A description of the samples used in the lung cancer testingpanel is provided in Table 3 below. A description of the samples used inthe breast cancer testing panel is provided in Table 4 and Table 4_(—)1below. Table 4_(—)2 provides a key for various terms listed in table4_(—)1. A description of the samples used in the normal tissue panel isprovided in Table 5 and table 5_(—)1 below.

TABLE 1 Tissue samples in ovarian cancer testing panel: Sample name Lotnumber Source Pathology Grade age 33-B-Pap Sero CystAde G1 A503175BioChain Serous papillary cystadenocarcinoma 1 41 41-G-Mix Sero/Muc/EndoG2 98-03-G803 GOG Mixed epithelial cystadenocarcinoma with mucinous, 238 endometrioid, squamous and papillary serous (Stage 2) 35-G-Endo AdenoG2 94-08-7604 GOG Endometrioid adenocarcinoma 2 39 14-B-Adeno G2 A501111BioChain Adenocarcinoma 2 41 12-B-Adeno G3 A406023 BiochainAdenocarcinoma 3 45 40-G-Mix Sero/Endo G2 95-11-G006 GOG Papillaryserous and endometrioid cystadenocarcinoma 2 49 (Stage 3C) 4-A-PapCystAdeno G2 ILS-7286 ABS Papillary cystadenocarcinoma 2 50 3-A-PapAdeno G2 ILS-1431 ABS Papillary adenocarcinoma 2 52 2-A-Pap Adeno G2ILS-1408 ABS Papillary adenocarcinoma 2 53 5-G-Adeno G3 99-12-G432 GOGAdenocarcinoma (Stage 3C) 3 46 11-B-Adeno G3 A407068 BiochainAdenocarcinoma 3 49 39--G-Mix Sero/Endo G3 2001-12-G037 GOG Mixed serousand endometrioid adenocarcinoma 3 49 29-G-Sero Adeno G3 2001-12-G035 GOGSerous adenocarcinoma (Stage 3A) 3 50 70-G-Pap Sero Adeno G3 95-08-G069GOG Papillary serous adenocarcinoma 3 50 6-A-Adeno G3 A0106 ABSadenocarcinoma 3 51 31-B-Pap Sero CystAde G3 A503176 BioChain Serouspapillary cystadenocarcinoma 3 52 25-A-Pap Sero Adeno G3 N0021 ABSPapillary serous adenocarcinoma (Stage T3CN1MX) 3 55 37-G-Mix Sero/EndoG3 2002-05-G513 GOG Mixed serous and endometrioid adenocarcinoma 3 567-A-Adeno G3 IND-00375 ABS adenocarcinoma 3 59 8-B-Adeno G3 A501113BioChain adenocarcinoma 3 60 10-B-Adeno G3 A407069 BiochainAdenocarcinoma 3 60 38-G-Mix Sero/Endo G3 2002-05-G509 GOG Mixed serousand endometrioid adenocarcinoma of mullerian 3 64 (Stage 3C) 13-G-AdenoG3 94-05-7603 GOG Poorly differentiated adenocarcinoma from primaryperitoneal 3 67 24-G-Pap Sero Adeno G3 2001-07-G801 GOG Papillary serousadenocarcinoma 3 68 34-G-Pap Endo Adeno G3 95-04-2002 GOG Papillaryendometrioid adenocarcinoma (Stage 3C) 3 68 30-G-Pap Sero Adeno G32001-08-G011 GOG Papillary serous carcinoma (Stage 1C) 3 72 1-A-PapAdeno G3 ILS-1406 ABS Papillary adenocarcinoma 3 73 9-G-Adeno G399-06-G901 GOG Adenocarcinoma (maybe serous) 3 84 32-G-Pap Sero CystAdeG3 93-09-4901 GOG Serous papillary cystadenocarcinoma 3 67 66-G-Pap SeroAdeno G3 SIV 2000-01-G413 GOG Papillary serous carcinoma (metastais ofprimary peritoneum) 3 67 (Stage 4) 19-B-Muc Adeno G3 A504085 BioChainMucinous adenocarcinoma 3 34 21-G-Muc CystAde G2-3 95-10-G020 GOGMucinous cystadenocarcinoma (Stage 2) 2-3 44 18-B-Muc Adeno G3 A504083BioChain Mucinous adenocarcinoma 3 45 20-A-Pap Muc CystAde USA-00273 ABSPapillary mucinous cystadenocarcinoma 46 17-B-Muc Adeno G3 A504084BioChain Mucinous adenocarcinoma 3 51 22-A-Muc CystAde G2 A0139 ABSMucinous cystadenocarcinoma (Stage 1C) 2 72 43-G-Clear cell Adeno G32001-10-G002 GOG Clear cell adenocarcinoma 3 74 44-G-Clear cell Adeno2001-07-G084 GOG Clear cell adenocarcinoma (Stage 3A) 73 15-B-Adeno G3A407065 BioChain Carcinoma 3 27 16-Ct-Adeno 1090387 Clontech CarcinomaNOS NA 58 23-A-Muc CystAde G3 VNM-00187 ABS Mucinous cystadenocarcinomawith low malignant 3 45 42-G-Adeno borderline 98-08-G001 GOG Epithelialadenocarcinoma of borderline malignancy 46 63-G-Sero CysAdenoFibroma2000-10-G620 GOG Serous CysAdenoFibroma of borderline malignancy 7162-G-Ben Muc CysAdenoma 99-10-G442 GOG Benbin mucinus cysadenoma 3260-G-Muc CysAdenoma 99-01-G043 GOG Mucinous Cysadenoma 40 56-G-Ben MucCysAdeno 99-01-G407 GOG Bengin mucinus cysadenoma 46 64-G-Ben SeroCysAdenoma 99-06-G039 GOG Bengin Serous CysAdenoma 57 61-G-MucCysAdenoma 99-07-G011 GOG Mucinous Cysadenoma 63 59-G-SeroCysAdenoFibroma 98-12-G401 GOG Serous CysAdenoFibroma 77 51-G-N M4198-03-G803N GOG Normal (matched tumor 98-03-G803) 38 75-G-N M6099-01-G043N GOG Normal (matched tumor 99-01-G043) 40 49-B-N M14 A501112BioChain Normal (matched tumor A501111) 41 52-G-N M42 98-08-G001N GOGNormal (matched tumor 98-08-G001) 46 68-G-N M56 99-01-G407N GOG Normal(matched bengin 99-01-G407) 46 50-B-N M8 A501114 BioChain Normal(matched tumor A501113) 60 67-G-N M38 2002-05-509N GOG Normal (matchedtumor 2002-05-G509) 64 69-G-N M24 2001-07-G801N GOG Normal (matchedtumor 2001-07-G801) 68 73-G-N M59 98-12-G401N GOG Normal (matched tumor98-12-G401) 77 72-G-N M66 2000-01-G413N GOG Normal (matched tumor2000-01-G413) 45-B-N A503274 BioChain Normal PM 41 46-B-N A504086BioChain Normal PM 41 71-CG-N CG-188-7 Ichilov Normal PM 49 48-B-NA504087 BioChain Normal PM 51

TABLE 2 Tissue samples in colon cancer testing panel sample name Lot No.tissue source pathology Grade gender/age 58-B-Adeno G1 A609152 Colonbiochain Adenocarcinoma 1 M/73 59-B-Adeno G1 A609059 Colon biochainAdenocarcinoma, Ulcer 1 M/58 14-CG-Polypoid Adeno G1 D-C CG-222 (2)Rectum Ichilov Well polypoid adeocarcinoma Duke's C F/49 17-CG-AdenoG1-2 CG-163 Rectum Ichilov Adenocarcinoma 2 M/73 10-CG-Adeno G1-2 D-B2CG-311 Sigmod colon Ichilov Adenocarcinoma Astler-Coller B2. 1-2 M/8811-CG-Adeno G1-2 D-C2 CG-337 Colon Ichilov Adenocarcinoma Astler-CollerC2. 1-2 NA 6-CG-Adeno G1-2 D-C2 CG-303 (3) Colon Ichilov AdenocarcinomaAstler-Coller C2. 1-2 F/77 5-CG-Adeno G2 CG-308 Colon Sigma IchilovAdenocarcinoma. 2 F/80 16-CG-Adeno G2 CG-278C colon IchilovAdenocarcinoma 2 F/60 56-B-Adeno G2 A609148 Colon biochainAdenocarcinoma 2 F48 61-B-Adeno G2 A606258 Colon biochainAdenocarcinoma, Ulcer 2 M/41 60-B-Adeno G2 A609058 Colon biochainAdenocarcinoma, Ulcer 2 M/67 22-CG-Adeno G2 D-B CG-229C Colon IchilovAdenocarcinoma Duke's B 2 F/55 1-CG-Adeno G2 D-B2 CG-335 Cecum IchilovAdenocarcinoma Dukes B2. 2 F/66 12-CG-Adeno G2 D-B2 CG-340 Colon SigmaIchilov Adenocarcinoma Astler-Coller B2. 2 M/66 28-CG-Adeno G2 D-B2CG-284 sigma Ichilov Adenocarcinoma Duke's B2 2 F/72 2-CG-Adeno G2 D-C2CG-307 X2 Cecum Ichilov Adenocarcinoma Astler-Coller C2. 2 F/899-CG-Adeno G2 D-D CG-297 X2 Rectum Ichilov Adenocarcinoma Dukes D. 2M/62 13-CG-Adeno G2 D-D CG-290 X2 Rectosigmoidal colon IchilovAdenocarcinoma Dukes D. 2 M/47 26-CG-Adeno G2 D-D CG-283 sigma IchilovColonic adenocarcinoma Duke's D 2 F/63 4-CG-Adeno G3 CG-276 ColonIchilov Carcinoma. 3 M/64 53-B-Adeno G3 A609161 Colon biochainAdenocarcinoma 3 F/53 54-B-Adeno G3 A609142 Colon biochainAdenocarcinoma 3 M/53 55-B-Adeno G3 A609144 Colon biochainAdenocarcinoma 3 M/68 57-B-Adeno G3 A609150 Colon biochainAdenocarcinoma 3 F/45 72-CG-Adeno G3 CG-309 colon Ichilov Adenocarcinoma3 F/88 20-CG-Adeno G3 D-B2 CG-249 Colon Ichilov Ulcerated adenocarcinomaDuke's B2 3 M/36 7-CG-Adeno D-A CG-235 Rectum Ichilov Adenocarcinomaintramucosal Duke's F/66 A. 23-CG-Adeno D-C CG-282 sigma Ichilov Mucinusadenocarcinoma Astler Coller C M/51 3-CG-Muc adeno D-D CG-224 ColonIchilov Mucinois adenocarcinoma Duke's D M/48 18-CG-Adeno CG-22C ColonIchilov Adenocarcinoma NA 19-CG-Adeno CG-19C (1) Colon IchilovAdenocarcinoma NA 21-CG-Adeno CG-18C Colon Ichilov Adenocarcinoma NA24-CG-Adeno CG-12 (2) Colon Ichilov Adenocarcinoma NA 25-CG-Adeno CG-2Colon Ichilov Adenocarcinoma NA 27-CG-Adeno CG-4 Colon IchilovAdenocarcinoma NA 8-CG-diverticolosis, diverticulitis CG-291 Wall ofsigma Ichilov Diverticolosis and F/65 diverticulitis of the Colon46-CG-Crohn's disease CG-338C Cecum Ichilov Crohn's disease M/2247-CG-Crohn's disease CG-338AC Colon Ichilov Crohn's disease. M/2242-CG-N M20 CG-249N Colon Ichilov Normal M/36 43-CG-N M8 CG-291N Wall ofsigma Ichilov Normal F/65 44-CG-N M21 CG-18N Colon Ichilov Normal NA45-CG-N M11 CG-337N Colon Ichilov Normal M/75 49-CG-N M14 CG-222N RectumIchilov Normal F/49 50-CG-N M5 CG-308N Sigma Ichilov Within normallimits F/80 51-CG-N M26 CG-283N Sigma Ichilov Normal F/63 41-B-N A501156Colon biochain Normal PM M/78 52-CG-N CG-309TR Colon Ichilov Withinnormal limits F/88 62-B-N A608273 Colon biochain Normal PM M/66 63-B-NA609260 Colon biochain Normal PM M/61 64-B-N A609261 Colon biochainNormal PM F/68 65-B-N A607115 Colon biochain Normal PM M/24 66-B-NA609262 Colon biochain Normal PM M/58 67-B-N A406029 Colon biochainNormal PM (Pool of 10) 69-B-N A411078 Colon biochain Normal PM (Pool of10) F&M 70-Cl-N 1110101 Colon clontech Normal PM (Pool of 3) 71-Am-N071P10B Colon Ambion Normal (IC BLEED) F/34

TABLE 3 Tissue samples in lung cancer testing panel sample name Lot No.source pathology Grade gender/age 1-B-Adeno G1 A504117 BiochainAdenocarcinoma 1 F/29 2-B-Adeno G1 A504118 Biochain Adenocarcinoma 1M/64 95-B-Adeno G1 A610063 Biochain Adenocarcinoma 1 F/54 12-B-Adeno G2A504119 Biochain Adenocarcinoma 2 F/74 75-B-Adeno G2 A609217 BiochainAdenocarcinoma 2 M/65 77-B-Adeno G2 A608301 Biochain Adenocarcinoma 2M/44 13-B-Adeno G2-3 A504116 Biochain Adenocarcinoma 2-3 M/64 89-B-AdenoG2-3 A609077 Biochain Adenocarcinoma 2-3 M/62 76-B-Adeno G3 A609218Biochain Adenocarcinoma 3 M/57 94-B-Adeno G3 A610118 BiochainAdenocarcinoma 3 M/68 3-CG-Adeno CG-200 Ichilov Adenocarcinoma NA14-CG-Adeno CG-111 Ichilov Adenocarcinoma M/68 15-CG-Bronch adeno CG-244Ichilov Bronchioloalveolar adenocarcinoma M/74 45-B-Alvelous AdenoA501221 Biochain Alveolus carcinoma F/50 44-B-Alvelous Adeno G2 A501123Biochain Alveolus carcinoma 2 F/61 19-B-Squamous G1 A408175 BiochainSquamous carcinoma 1 M/78 16-B-Squamous G2 A409091 Biochain Squamouscarcinoma 2 F/68 17-B-Squamous G2 A503183 Biochain Squamous carcinoma 2M/57 21-B-Squamous G2 A503187 Biochain Squamous carcinoma 2 M/5278-B-Squamous G2 A607125 Biochain Squamous Cell Carcinoma 2 M/6280-B-Squamous G2 A609163 Biochain Squamous Cell Carcinoma 2 M/7418-B-Squamous G2-3 A503387 Biochain Squamous Cell Carcinoma 2-3 M/6381-B-Squamous G3 A609076 Biochain Squamous Carcinoma 3 m/5379-B-Squamous G3 A609018 Biochain Squamous Cell Carcinoma 3 M/6720-B-Squamous A501121 Biochain Squamous Carcinoma M/64 22-B-SquamousA503386 Biochain Squamous Carcinoma M/48 88-B-Squamous A609219 BiochainSquamous Cell Carcinoma M/64 100-B-Squamous A409017 Biochain SquamousCarcinoma M/64 23-CG-Squamous CG-109 (1) Ichilov Squamous Carcinoma M/6524-CG-Squamous CG-123 Ichilov Squamous Carcinoma M/76 25-CG-SquamousCG-204 Ichilov Squamous Carcinoma M/72 87-B-Large cell G3 A609165Biochain Large Cell Carcinoma 3 F/47 38-B-Large cell A504113 BiochainLarge cell M/58 39-B-Large cell A504114 Biochain Large cell F/3582-B-Large cell A609170 Biochain Large Cell Neuroendocrine CarcinomaM/68 30-B-Small cell carci G3 A501389 Biochain small cell 3 M/3431-B-Small cell carci G3 A501390 Biochain small cell 3 F/59 32-B-Smallcell carci G3 A501391 Biochain small cell 3 M/30 33-B-Small cell carciG3 A504115 Biochain small cell 3 M 86-B-Small cell carci G3 A608032Biochain Small Cell Carcinoma 3 F/52 83-B-Small cell carci A609162Biochain Small Cell Carcinoma F/47 84-B-Small cell carci A609167Biochain Small Cell Carcinoma F/59 85-B-Small cell carci A609169Biochain Small Cell Carcinoma M/66 46-B-N M44 A501124 Biochain NormalM44 F/61 47-B-N A503205 Biochain Normal PM M/26 48-B-N A503206 BiochainNormal PM M/44 49-B-N A503384 Biochain Normal PM M/27 50-B-N A503385Biochain Normal PM M/28 90-B-N A608152 Biochain Normal (Pool 2) PM pool2 91-B-N A607257 Biochain Normal (Pool 2) PM pool 2 92-B-N A503204Biochain Normal PM m/28 93-Am-N 111P0103A Ambion Normal PM F/61 96-Am-N36853 Ambion Normal PM F/43 97-Am-N 36854 Ambion Normal PM M/46 98-Am-N36855 Ambion Normal PM F/72 99-Am-N 36856 Ambion Normal PM M/31

TABLE 4 Tissue samples in breast cancer testing panel sample name Lot nosource pathology grade age TNM stage 14-A-IDC G2 A0135T ABS IDC 2 37T2N2Mx 43-B-IDC G2 A609183 Biochain IDC 2 40 54-B-IDC G2 A605353Biochain IDC 2 41 55-B-IDC G2 A609179 Biochain IDC 2 42 47-B-IDC G2A609221 Biochain IDC 2 42 17-A-IDC G2 4904020036T ABS IDC 2-3 42 T3N1Mx42-A-IDC G3 6005020031T ABS IDC 3 42 T1cN0Mx 7-A-IDC G2 7263T ABS IDC 243 T1N0M0 stage 1 48-B-IDC G2 A609222 Biochain IDC 2 44 53-B-IDC G2A605151 Biochain IDC 2 44 12-A-IDC G2 1432T ABS IDC 2 46 T2N0M0 stage 2A61-B-IDC G2 A610029 Biochain IDC 2 46 46-B-Carci G2 A609177 BiochainCarcinoma 2 48 16-A-IDC G2 4904020032T ABS IDC 2 49 T3N1Mx 62-B-IDC G2A609194 Biochain IDC 2 51 49-B-IDC G2 A609223 Biochain IDC 2 54 32-A-MucCarci 7116T ABS Mucinous carcinoma 54 T2N0M0 stage 2A 45-B-IDC G2A609181 Biochain IDC 2 58 15-A-IDC G2 7259T ABS IDC 2 59 T3N1M0 stage 3A52-B-ILC G1 A605360 Biochain Invasive Lobular Carcinoma 1 60 6-A-IDC G17238T ABS IDC 1 60 T2N0M0 stage 2A 26-A-IDC G3 7249T ABS IDC 3 60 T2N0M0stage 2A 13-A-IDC G2 A0133T ABS IDC 2 63 T2N1aMx 50-B-IDC G2 A609224Biochain IDC 2 69 44-B-IDC G2 A609198 Biochain IDC 2 77 51-B-IDC G1A605361 Biochain IDC 1 79 31-CG-IDC CG-154 Ichilov IDC 83 27-A-IDC G34907020072T ABS IDC 3 91 T2N0Mx 36-A-N M7 7263N ABS Normal matched to 7T43 40-A-N M12 1432N ABS Normal matched to 12T 46 39-A-N M15 7259N ABSNormal matched to 15T 59 35-A-N M6 7238N ABS Normal matched to 6T 6041-A-N M26 7249N ABS Normal matched to 26T 60 57-B-N A609233 BiochainNormal PM 34 59-B-N A607155 Biochain Normal PM 35 60-B-N A609234Biochain Normal PM 36 63-Am-N 26486 Ambion Normal PS 43 66-Am-N 36678Ambion Normal PM 45 64-Am-N 23036 Ambion Normal PM 57 56-B-N A609235Biochain Normal PM 59 65-Am-N 31410 Ambion Normal PM 63 67-Am-N073P01060286A Ambion Normal PM 64 58-B-N A609232 Biochain Normal PM 65

TABLE 4_1 Tissue samples in Breast cancer testing panel sample_id (GCI)/case id (Asterand)/ Age Re- Source/ lot no. TISSUE_ID Sample # of cov-Year De- sample (old (GCI)/specimen ID SampD C Tum WT HT Ethnic # ofLive first Br ery of Tissue livery name samples) ID(Asterand) (Asterand)IAG Grade TNM Stage % age MS (KG) (CM) BMI B Preg. Bir child child Typebirth BC_in- Aster 1-As-DCIS 19723 42509 42509A1 DCIS High T1aN0M0 0 10039 Pre-M 102 157 41.4 CAU 2 1 Surg situ S0 Grade BC GCI 2-GC-IDC 5IRTK5IRTKAXT IDC I 75 39 Pre-M 48.1 147 22.2 WCAU 1 0 — — Surg 1962 SI BCABS 3-(42)-AB- 6005020031T IDC 3 T1cN0Mx I 42 IDC SI BC ABS 4-(7)-AB-7263T IDC 2 T1N0M0 I 43 IDC SI BC GCI 5-GC-IDC DSI52 DSI52AH3 IDC I 5050 Post-M 113.4 175 36.9 WCAU 2 2 17 0 Surg 1951 SI BC GCI 6-GC-IDCS2GBY S2GBYAGC IDC I 55 56 Post-M 57.6 168 20.5 WCAU 0 — — — Surg 1945SI BC GCI 7-GC-IDC POPHP POPHPAZ4 IDC I 65 57 Post-M 76.2 165 28.0 WCAU2 2 17 0 Surg 1944 SI BC GCI 8-GC-IDC I2YLE I2YLEACP IDC I 65 60 Post-M68 140 34.8 WCAU 1 1 23 0 Surg 1942 SI BC Aster 9-As-IDC SI 17959 3122531225A1 IDC 2 T1NXM0 I 90 65 Post-M 70 168 24.8 CAU 3 2 Aut BC ABS10-(12)-AB- 1432T IDC 2 T2N0M0 IIA 46 IDC SIIA BC Aster 11-As-IDC 1713830697 30697A1 IDC 3 T2NXM0 IIA 90 46 Pre-M 69 174 22.8 CAU 1 1 Surg SIIABC GCI 12-GC-IDC YSZ67 YSZ67A48 IDC IIA 70 46 Pre-M 76.2 165 28.0 WCAU 10  0 0 Surg 1956 SIIA BC ABS 13-(6)-AB- 7238T IDC 1 T2N0M0 IIA 60 IDCSIIA BC ABS 14-(26)-AB- 7249T IDC 3 T2N0M0 IIA 60 IDC SIIA BC GCI15-GC-IDC UT3SE UT3SEAQY IDC IIA 80 67 Post-M 113.4 168 40.4 WCAU 3 1 340 Surg 1938 SIIA BC GCI 16-GC-IDC PVSYX PVSYXA72 IDC IIA 65 70 Pre-M79.4 163 30.0 WCAU 2 2 20 0 Surg 1932 SIIA BC GCI 17-GC-IDC GETCVGETCVAY2 IDC IIA 55 70 Post-M 72.6 163 27.5 WCAU 2 2 21 0 Surg 1931 SIIABC ABS 18-(27)-AB- 4907020072T IDC 3 T2N0Mx IIA 91 IDC SIIA BC GCI19-GC-IDC SE5BK SE5BKAEQ IDC IIB 55 41 Pre-M 61.2 165 22.5 WCAU 0 — — —Surg 1960 SIIB BC GCI 20-GC-IDC OLKL4 OLKL4AO6 IDC IIB 60 46 Pre-M 111.1168 39.5 WCAU 2 2 24 2 Surg 1955 SIIB BC GCI 21-GC-IDC VK1EJ VK1EJAQEIDC IIB 60 54 Post-M 72.6 168 25.8 WCAU 0 — — — Surg 1947 SIIB BC GCI22-GC-IDC 3Z5Z4 3Z5Z4ANH IDC IIB 85 60 Post-M 80 163 30.3 WCAU 1 1 22 0Surg 1942 SIIB BC ABS 23-(13)-AB- A0133T IDC 2 T2N1aMx IIB 63 IDC SIIBBC GCI 24-GC-IDC J5MPN J5MPNA9Q IDC IIB 55 64 Post-M 68.5 157 27.6 WCAU4 3 25 3 Surg 1938 SIIB BC GCI 25-GC-IDC 54NTA 54NTAAKT IDC IIB 70 67Post-M 56.7 160 22.1 WCAU 5 5 20 0 Surg 1934 SIIB BC GCI 27-GC-IDC RD3F9RD3F9AFQ IDC IIIA 90 41 ? 63.5 157 25.6 WCAU 1 1 25 0 Surg 1962 SIIIA BCABS 28-(17)-AB- 4904020036T IDC 2-3 T3N1Mx IIIA 42 IDC SIIIA BC ABS29-(16)-AB- 4904020032T IDC 2 T3N1Mx IIIA 49 IDC IIIA BC ABS 30-(15)-AB-7259T IDC 2 T3N1M0 IIIA 59 IDC SIIIA BC GCI 31-GC-IDC YOLOF YOLOFARG IDCIIIA 85 62 Post-M 82.6 160 32.2 WCAU 3 3 20 0 Surg 1943 SIIIA BC GCI32-GC-IDC 4W2NY 4W2NYAC1 IDC IIIB 50 39 Pre-M 54.4 163 20.6 WCAU 2 2 260 Surg 1962 SIIIB BC GCI 33-GC-IDC YQ1WW YQ1WWAUV IDC IIIB 60 62 Pre-M78 163 29.5 WCAU 0 — — — Surg 1940 SIIIB BC GCI 34-GC-IDC KIOE7 KIOE7AI9IDC IIIB 55 65 Post-M 73.5 157 29.6 WCAU 2 2 18 2 Surg 1939 SIIIB BCBioch 70-(43)-Bc- A609183 IDC 2 40 IDC BC Bioch 71-(54)-Bc- A605353 IDC2 41 IDC BC ABS 72-(55)-Bc- A609179 IDC 2 42 IDC BC Bioch 73-(47)-Bc-A609221 IDC 2 42 IDC BC Bioch 74-(48)-Bc- A609222 IDC 2 44 IDC BC Bioch75-(53)-Bc- A605151 IDC 2 44 IDC BC Bioch 76-(61)-Bc- A610029 IDC 2 46IDC BC Bioch 77-(46)-Bc- A609177 Carc 2 48 Carci BC Ichilov 78-(62)-Bc-A609194 IDC 2 51 IDC BC Amb 79-(32)-AB- 7116T MC T2N0M0 IIA 54 Muc CarciSIIA BC GCI 80-(49)-Bc- A609223 IDC 2 54 IDC BC GCI 81-(45)-Bc- A609181IDC 2 58 IDC BC GCI 82-(50)-Bc- A609224 IDC 2 69 IDC BC Bioch83-(44)-Bc- A609198 IDC 2 77 IDC BC Bioch 84-(51)-Bc- A605361 IDC 1 79IDC BC Amb 85-(31)-Ic- CG-154 IDC 83 IDC BC Aster 35-As-ILC 17090 3073830738A1 ILC T1cNXM0 I 100 50 94 170 32.5 W 2 2 Surg SI BC GCI 36-GC-ILCI35US I35USA9G ILC IIA 60 70 77.1 178 24.4 WCAU — — — — Surg 1932 SIIABC GCI 37-GC-ILC IS84Y IS84YAAY ILC IIB 65 67 Post-M 62.6 163 23.7 WCAU2 2 16 0 Surg 1934 SIIB BC Bioch 38-(52)-Bc- A605360 ILC 1 60 ILC BBAster 39-As-Ben 11975 15478 15478B1 FIBR 100 24 Pre-M 80 164 29.7 CAU 20 Surg BB GCI 40-GC-Ben ZT15M ZT15MAMR FIBR 100 34 57.6 165 21.1 WCAUSurg 1967 BB GCI 41-GC-Ben NNP3Q NNP3QA4V FIBR 95 54 56.7 157 22.9 WCAUSurg 1948 BB GCI 42-GC-Ben QK8IY QK8IYALU FIBR 100 41 59 173 19.7 WCAUSurg 1960 BN-PS GCI 43-GC-N 83LO7 83LO7NEH NB-PS 32 78.5 155 32.7 WCAUSurg 1969 PS BN-PS GCI 45-GC-N O6JBJ O6JBJNT1 NB-PS 38 67.1 173 22.5WCAU Surg 1963 PS BN-PS GCI 46-GC-N E6UDD E6UDDNCF NB-PS 40 99.8 17034.5 WCAU Surg 1961 PS BN-PS GCI 47-GC-N DHLR1 DHLR1NIQ NB-PS 40 90.7168 32.3 WCAU Surg 1961 PS BN-PS GCI 48-GC-N JHQEH JHQEHN4D NB-PS 4165.3 157 26.3 WCAU Surg 1960 PS BN-PS Amb 49-(63)-Am- 26486 NB-PS 43 NPS BN-PS GCI 50-GC-N ONBFK ONBFKNO2 NB-PS 45 81.6 165 30.0 WCAU Surg1956 PS BN-PS GCI 51-GC-N TG6J6 TG6J6NNA NB-PS 46 90.7 173 30.4 WCAUSurg 1955 PS BN-PS Aster 52-GC-N 14398 20021 20021D1 NB-PS 49 Pre-M 68165 25.0 CAU 3 3 Surg PS BN-PS GCI 54-GC-N AJGXV AJGXVNFC NB-PS 52 70168 24.8 WCAU Surg 1949 PS BN-PS GCI 56-GC-N HLCZX HLCZXNLS NB-PS 54 67163 25.2 WCAU Surg 1947 PS BN-PS GCI 58-GC-N FGV8P FGV8PNQ6 NB-PS 61106.6 168 37.9 WCAU Surg 1940 PS BN-? Aster 59-As-N PS 9264 9486 9486A1NB-PS 0 0 0 0.0 BN-PM Bioch 60-(57)-Bc- A609233 A609233 NB-PM 34 Aut NPM BN-PM Bioch 61-(59)-Bc- A607155 A607155 NB-PM 35 Aut N PM BN-PM Bioch62-(60)-Bc- A609234 A609234 NB-PM 36 Aut N PM BN-PM Amb 63-(66)-Am-36678 36678 NB-PM 45 Aut N PM BN-PM Amb 64-(64)-Am- 23036 23036 NB-PM 57Aut N PM BN-PM Amb 65-(65)-Am- 31410 31410 NB-PM 63 Aut N PM BN-PM Amb66-(67)-Am- 073P010602086A 073P010602086A NB-PM 64 Aut N PM BN-PM Bioch67-(58)-Bc- A609232 A609232 NB-PM 65 Aut N PM BN-PM Aster 68-As-N 88628766 8766B1 NB-PM 74 64 157 26.0 CAU Aut PM BN-PM Aster 69-As-N 84577928 7928M1 NB-PM 87 59 165 21.7 CAU Aut PM

TABLE 4_2 Key Full Name # Live Bir # Live Births # of Preg Number ofPregnancies Amb Ambion Aster Asterand Aut Autopsy BB Breast Benign BCBreast Cancer Bioch Biochain BN Breast Normal BN-PM Breast_Normal-PMBN-PS Breast_Normal-PS Breastfeed child Br Child C Stage Cancer StageCarc Carcinoma CAU Caucasian DCIS Ductal Carcinoma In Situ Ethnic BEthnic Background FIBR FIBROADENOMA IDC INFILTRATING DUCTAL CARCINOMAILC INFILTRATING LOBULAR CARCINOMA M Menopausal MC Mucinous carcinoma MSMenopausal Status NB-PM NORMAL BREAST-PM NB-PS NORMAL BREAST-PS Post-MPost-Menopausal Pre-M Pre-Menopausal Samp DIAG Sample Diagnosis SurgSurgical Tum % Percentage of Tumor W White WCAU White Caucasian

TABLE 5 Tissue samples in normal panel: Lot no. Source Tissue PathologySex/Age comments 1-Am-Colon (C71) 071P10B Ambion Colon PM IC bleed F/43IC-intracarnial bleed 2-B-Colon (C69) A411078 Biochain Colon PM-Pool of10 M (26-78)&F (53-77) 3-Cl-Colon (C70) 1110101 Clontech Colon PM-Poolof 3 sudden death M&F (20-50) 4-Am-Small Intestine 091P0201A AmbionSmall Intestine PM ICH M/85 5-B-Small Intestine A501158 Biochain SmallIntestine PM M/63 6-B-Rectum A605138 Biochain Rectum PM M/25 7-B-RectumA610297 Biochain Rectum PM M/24 8-B-Rectum A610298 Biochain Rectum PMM/27 9-Am-Stomach 110P04A Ambion Stomach PM GSW M/16 10-B-StomachA501159 Biochain Stomach PM M/24 11-B-Esophagus A603814 BiochainEsophagus PM M/26 12-B-Esophagus A603813 Biochain Esophagus PM M/4113-Am-Pancreas 071P25C Ambion Pancreas PM MVA F/25 14-CG-PancreasCG-255-2 Ichilov Pancreas PM M/75 15-B-Lung A409363 Biochain LungPM-Pool of 5 M (24-28)&F62 16-Am-Lung (L93) 111P0103A Ambion Lung PM ICHF/61 17-B-Lung (L92) A503204 Biochain Lung PM M/28 19-B-Ovary (O48)A504087 Biochain Ovary PM F/51 20-B-Ovary (O46) A504086 Biochain OvaryPM F/41 75-G-Ovary L629FRV1 GCI Ovary PS DIGESTIVE HEMORRHAGE F/47(ALCOHOLISM) 76-G-Ovary DWHTZRQX GCI Ovary PS LEIOMYOMAS F/42 77-G-OvaryFDPL9NJ6 GCI Ovary PS VAGINAL BLEEDING F/56 78-G-Ovary GWXUZN5M GCIOvary PS ABNORMAL PAP SMEARS F/53 21-Am-Cervix 101P0101A Ambion CervixPM Surgery F/40 23-B-Cervix A504089 Biochain Cervix PM-Pool of 5 F(36-55) 24-B-Uterus A411074 Biochain Uterus PM-Pool of 10 F (32-53)25-B-Uterus A409248 Biochain Uterus PM F/35 26-B-Uterus A504090 BiochainUterus PM-Pool of 5 F (40-53) 28-Am-Bladder 071P02C Ambion Bladder PMGSW M/28 29-B-Bladder A504088 Biochain Bladder PM-Pool of 5 M(26-44)&F30 30-Am-Placenta 021P33A Ambion Placenta PB F/33 PB - postbirth 31-B-Placenta A410165 Biochain Placenta PB F/26 32-B-PlacentaA411073 Biochain Placenta PB-Pool of 5 F (24-30) 33-B-Breast (B59)A607155 Biochain Breast PM F/36 34-Am-Breast (B63) 26486 Ambion BreastPS bilateral breast reduction F/43 35-Am-Breast (B64) 23036 AmbionBreast PM lung cancer F/57 36-Cl-Prostate (P53) 1070317 ClontechProstate PM-Pool of 47 sudden death M (14-57) 37-Am-Prostate (P42)061P04A Ambion Prostate PM IC bleed M/47 38-Am-Prostate (P59) 25955Ambion Prostate PM head trauma M/62 39-Am-Testis 111P0104A Ambion TestisPM GSW M/25 40-B-Testis A411147 Biochain Testis PM M/74 41-Cl-Testis1110320 Clontech Testis PM-Pool of 45 sudden death M (14-64)42-CG-Adrenal CG-184-10 Ichilov Adrenal PM F/81 43-B-Adrenal A610374Biochain Adrenal PM F/83 44-B-Heart A411077 Biochain Heart PM-Pool of 5M (23-70) 45-CG-Heart CG-255-9 Ichilov Heart focal PM M/75 fibrosis46-CG-Heart CG-227-1 Ichilov Heart PM F/36 47-Am-Liver 081P0101A AmbionLiver PM ICH M/64 48-CG-Liver CG-93-3 Ichilov Liver PM F/19 49-CG-LiverCG-124-4 Ichilov Liver of fetus PM fetus 50-Cl-BM 1110932 Clontech BoneMarrow PM-Pool of 8 sudden death M&F (22-65) 51-CGEN-Blood WBC#5 CGENBlood — M 52-CGEN-Blood WBC#4 CGEN Blood — M 53-CGEN-Blood WBC#3 CGENBlood — M 54-CG-Spleen CG-267 Ichilov Spleen PM F/25 55-CG-Spleen111P0106B Ambion Spleen PM GSW M/25 56-CG-Spleen A409246 Biochain SpleenPM F/12 57-CG-Thymus CG-98-7 Ichilov Thymus PM F/28 58-Am-Thymus101P0101A Ambion Thymus PM head injury M/14 59-B-Thymus A409278 BiochainThymus PM M/28 60-B-Thyroid A610287 Biochain Thyroid PM M/2761-B-Thyroid A610286 Biochain Thyroid PM M/24 62-CG-Thyroid CG-119-2Ichilov Thyroid PM F/66 63-Cl-Salivary Gland 1070319 Clontech SalivaryGland PM-Pool of 24 sudden death M&F 15-60 64-Am-Kidney 111P0101B AmbionKidney PM ICH M 60 65-Cl-Kidney 1110970 Clontech Kidney PM-Pool of 14sudden death M&F 18-59 66-B-Kidney A411080 Biochain Kidney PM-Pool of 5M 24-46 67-CG-Cerebellum CG-183-5 Ichilov Cerebellum PM M/7468-CG-Cerebellum CG-212-5 Ichilov Cerebellum PM M/54 69-B-Brain A411322Biochain Brain PM M/28 70-Cl-Brain 1120022 Clontech Brain PM —71-B-Brain A411079 Biochain Brain PM-Pool of 2 M 27-28 72-CG-BrainCG-151-1 Ichilov Brain PM F/86 73-Am-Skeletal Muscle 101P013A AmbionSkeletal Muscle PM head injury F/28 74-Cl-Skeletal Muscle 1061038Clontech Skeletal Muscle PM-Pool of 2 sudden death M&F 43-46

TABLE 5_1 Normal panel 7-B-Rectum 1-(7)-Bc-Rectum Biochain A6102978-B-Rectum 2-(8)-Bc-Rectum Biochain A610298 new colon 3-GC-Colon GCICDSUV CDSUVNR3 new colon 4-As-Colon Asterand 16364 31802 31802B1 newcolon 5-As-Colon Asterand 22900 74446 74446B1 new small bowl 6-GC-Smallbowl GCI V9L7D V9L7DN6Z new small bowl 7-GC-Small bowl GCI M3GVTM3GVTN5R new small bowl 8-GC-Small bowl GCI 196S2 196S2AJN 9-Am-Stomach9-(9)-Am-Stomach Ambion 110P04A 10-B-Stomach 10-(10)-Bc-Stomach BiochainA501159 11-B-Esophagus 11-(11)-Bc-Esoph Biochain A603814 12-B-Esophagus12-(12)-Bc-Esoph Biochain A603813 new pancreas 13-As-Panc Asterand 89189442 9442C1 new pancreas 14-As-Panc Asterand 10082 11134 11134B148-CG-Liver 15-(48)-Ic-Liver Ichilov CG-93-3 new liver 16-As-LiverAsterand 7916 7203 7203B1 28-Am-Bladder 17-(28)-Am-Bladder Ambion071P02C 29-B-Bladder 18-(29)-Bc-Bladder Biochain A504088 64-Am-Kidney19-(64)-Am-Kidney Ambion 111P0101B 65-Cl-Kidney 20-(65)-Cl-KidneyClontech 1110970 66-B-Kidney 21-(66)-Bc-Kidney Biochain A411080 newkidney 22-GC-Kidney GCI N1EVZ N1EVZN91 new kidney 23-GC-Kidney GCI BMI6WBMI6WN9F 42-CG-Adrenal 24-(42)-Ic-Adrenal Ichilov CG-184-10 43-B-Adrenal25-(43)-Bc-Adrenal Biochain A610374 16-Am-Lung (L93) 26-(16)-Am-LungAmbion 111P0103A 17-B-Lung (L92) 27-(17)-Bc-Lung Biochain A503204 newlung 28-As-Lung Asterand 9078 9275 9275B1 new lung 29-As-Lung Asterand6692 6161 6161A1 new lung 30-As-Lung Asterand 7900 7180 7180F175-G-Ovary 31-(75)-GC-Ovary GCI L629FRV1 76-G-Ovary 32-(76)-GC-Ovary GCIDWHTZRQX 77-G-Ovary 33-(77)-GC-Ovary GCI FDPL9NJ6 78-G-Ovary34-(78)-GC-Ovary GCI GWXUZN5M 21-Am-Cervix 35-(21)-Am-Cerix Ambion101P0101A new cervix 36-GC-cervix GCI E2P2N E2P2NAP4 24-B-Uterus37-(24)-Bc-Uterus Biochain A411074 26-B-Uterus 38-(26)-Bc-UterusBiochain A504090 30-Am-Placenta 39-(30)-Am-Placen Ambion 021P33A32-B-Placenta 40-(32)-Bc-Placen Biochain A411073 new breast 41-GC-BreastGCI DHLR1 new breast 42-GC-Breast GCI TG6J6 new breast 43-GC-Breast GCIE6UDD E6UDDNCF 38-Am-Prostate (P59) 44-(38)-Am-Prostate Ambion 25955 addprostate from 45-Bc-Prostate Biochain A609258 prostate panel new testis46-As-Testis Asterand 13071 19567 19567B1 new testis 47-As-TestisAsterand 19671 42120 42120A1 ARTERY 48-GC-Artery GCI 7FUUP 7FUUPAMPARTERY 49-GC-Artery GCI YGTVY YGTVYAIN blood cells? 50-Th-Blood-MONOTel-Hashomer 52497 blood cells? 51-Th-Blood-MONO Tel-Hashomer 31055blood cells? 52-Th-Blood-MONO Tel-Hashomer 31058 54-CG-Spleen53-(54)-Ic-Spleen Ichilov CG-267 55-CG-Spleen 54-(55)-Ic-Spleen Ichilov111P0106B 57-CG-Thymus 55-(57)-Ic-Thymus Ichilov CG-98-7 58-Am-Thymus56-(58)-Am-Thymus Ambion 101P0101A 60-B-Thyroid 57-(60)-Bc-ThyroidBiochain A610287 62-CG-Thyroid 58-(62)-Ic-Thyroid Ichilov CG-119-2 newsalivary gland 59-Gc-Sali gland GCI NNSMV NNSMVNJC 67-CG-Cerebellum60-(67)-Ic-Cerebellum Ichilov CG-183-5 68-CG-Cerebellum61-(68)-Ic-Cerebellum Ichilov CG-212-5 69-B-Brain 62-(69)-Bc-BrainBiochain A411322 71-B-Brain 63-(71)-Bc-Brain Biochain A41107972-CG-Brain 64-(72)-Ic-Brain Ichilov CG-151-1 44-B-Heart65-(44)-Bc-Heart Biochain A411077 46-CG-Heart 66-(46)-Ic-Heart IchilovCG-227-1 45-CG-Heart (Fibrotic) 67-(45)-Ic-Heart (Fibrotic) IchilovCG-255-9 new skeletal muscle 68-GC-Skel Mus GCI T8YZS T8YZSN7O newskeletal muscle 69-GC-Skel Mus GCI Q3WKA Q3WKANCJ new skeletal muscle70-As-Skel Mus Asterand 8774 8235 8235G1 new skeletal muscle 71-As-SkelMus Asterand 8775 8244 8244A1 new skeletal muscle 72-As-Skel MusAsterand 10937 12648 12648C1 new skeletal muscle 73-As-Skel Mus Asterand6692 6166 6166A1

Materials and Experimental Procedures

RNA preparation—RNA was obtained from ABS (Wilmington, Del. 19801, USA,http://www.absbioreagents.com), BioChain Inst. Inc. (Hayward, Calif.94545 USA www.biochain.com), GOG for ovary samples—Pediatic CooperativeHuman Tissue Network, Gynecologic Oncology Group Tissue Bank, ChildrenHospital of Columbus (Columbus Ohio 43205 USA), Clontech (FranklinLakes, N.J. USA 07417, www.clontech.com), Ambion (Austin, Tex. 78744USA, http://www.ambion.com), Asternad (Detroit, Mich. 48202-3420, USA,www.asterand.com), and from Genomics Collaborative Inc. a Division ofSeracare (Cambridge, Mass. 02139, USA, www.genomicsinc.com).Alternatively, RNA was generated from tissue samples using TRI-Reagent(Molecular Research Center), according to Manufacturer's instructions.Tissue and RNA samples were obtained from patients or from postmortem.Total RNA samples were treated with DNaseI (Ambion).

RT PCR—Purified RNA (1 μg) was mixed with 150 ng Random Hexamer primers(Invitrogen) and 500 μM dNTP in a total volume of 15.6 μl. The mixturewas incubated for 5 min at 65° C. and then quickly chilled on ice.Thereafter, 5 μl of 5× SuperscriptII first strand buffer (Invitrogen),2.4 μl 0.1M DTT and 40 units RNasin (Promega) were added, and themixture was incubated for 10 min at 25° C., followed by furtherincubation at 42° C. for 2 min. Then, 1 μl (200 units) of SuperscriptII(Invitrogen) was added and the reaction (final volume of 25 μl) wasincubated for 50 min at 42° C. and then inactivated at 70° C. for 15min. The resulting cDNA was diluted 1:20 in TE buffer (10 mM Tris pH=8,1 mM EDTA pH=8).

Real-Time RT-PCR analysis—cDNA (5 μl), prepared as described above, wasused as a template in Real-Time PCR reactions using the SYBR Green Iassay (PE Applied Biosystem) with specific primers and UNG Enzyme(Eurogentech or ABI or Roche). The amplification was effected asfollows: 50° C. for 2 min, 95° C. for 10 min, and then 40 cycles of 95°C. for 15 sec, followed by 60° C. for 1 min. Detection was performed byusing the PE Applied Biosystem SDS 7000. The cycle in which thereactions achieved a threshold level (Ct) of fluorescence was registeredand was used to calculate the relative transcript quantity in the RTreactions. The relative quantity was calculated using the equationQ=efficiencŷ^(−Ct). The efficiency of the PCR reaction was calculatedfrom a standard curve, created by using serial dilutions of severalreverse transcription (RT) reactions. prepared from RNA purified from 5cell lines (HCT116, H1299, DU145, MCF7, ES-2). To minimize inherentdifferences in the RT reaction, the resulting relative quantities werenormalized to normalization factor calculated in one of the followingmethods as indicated in the text:

Method 1—the geometric mean of the relative quantities of the selectedhousekeeping (HSKP) genes was used as normalization factor.

Method 2—The expression of several housekeeping (HSKP) genes was checkedon every panel. The relative quantity (O) of each housekeeping gene ineach sample, calculated as described above, was divided by the medianquantity of this gene in all panel samples to obtain the “relative Q relto MED”. Then, for each sample the median of the “relative Q rel to MED”of the selected housekeeping genes was calculated and served asnormalization factor of this sample for further calculations. Schematicsummary of quantitative real-time PCR analysis is presented in FIG. 3.As shown, the x-axis shows the cycle number. The C_(T)=Threshold Cyclepoint, which is the cycle that the amplification curve crosses thefluorescence threshold that was set in the experiment. This point is acalculated cycle number in which PCR products signal is above thebackground level (passive dye ROX) and still in theGeometric/Exponential phase (as shown, once the level of fluorescencecrosses the measurement threshold, it has a geometrically increasingphase, during which measurements are most accurate, followed by a linearphase and a plateau phase; for quantitative measurements, the latter twophases do not provide accurate measurements). The y-axis shows thenormalized reporter fluorescence. It should be noted that this type ofanalysis provides relative quantification.

The sequences of the housekeeping genes measured in all the examples onthe ovary cancer tissue testing panel were as follows:

SDHA (GenBank Accession No. NM_004168 (SEQ ID NO: 364),) SDHA Forwardprimer (SEQ ID NO: 556): TGGGAACAAGAGGGCATCTG SDHA Reverse primer (SEQID NO: 557): CCACCACTGCATCAAATTCATG SDHA-amplicon (SEQ ID NO: 365):TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCAGTAGTGGATCATGAATTTGATGCAGTGGTGG PBGD (GenBank Accession No.BC019323 (SEQ ID NO: 381),), PBGD Forward primer (SEQ ID NO: 558):TGAGAGTGATTCGCGTGGG PBGD Reverse primer (SEQ ID NO: 559):CCAGGGTACGAGGCTTTCAAT PBGD-amplicon (SEQ ID NO: 382):TGAGAGTGATTCGCGTGGGTACCCGCAAGAGCCAGCTTGCTCGCATACAGACGGACAGTGTGGTGGCAACATTGAAAGCCTCGTACCCTGG HPRT1 (GenBank Accession No.NM_000194 (SEQ ID NO: 379), HPRT1 Forward primer (SEQ ID NO: 560):TGACACTGGCAAAACAATGCA HPRT1 Reverse primer (SEQ ID NO: 561):GGTCCTTTTCACCAGCAAGCT HPRT1-amplicon (SEQ ID NO: 380):TGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACC GAPDH (GenBank AccessionNo. BC026907 (SEQ ID NO: 451)) GAPDH Forward primer (SEQ ID NO: 562):TGCACCACCAACTGCTTAGC GAPDH Reverse primer (SEQ ID NO: 563):CCATCACGCCACAGTTTCC GAPDH-amplicon (SEQ ID NO: 450):TGCACCACCAACTGCTTAGCACCCCTGGCCAAGGTCATCCATGACAACTTTGGTATCGTGGAAGGACTCATGACCACAGTCCATGCCATCACTGCCACCC AGAAGACTGTGGATGG

The sequences of the housekeeping genes measured in all the examples oncolon cancer tissue testing panel were as follows:

PBGD (GenBank Accession No. BC019323 (SEQ ID NO: 381)), PBGD Forwardprimer (SEQ ID NO: 558): TGAGATGATTCGCGTGGG PBGD Reverse primer (SEQ IDNO: 559): CCAGGGTACGAGGCTTTCAAT PBGD-amplicon (SEQ ID NO: 382):TGAGAGTGATTCGCGTGGGTACCCGCAAGAGCCAGCTTGCTCGCATACAGACGGACAGTGTGGTGGCAACATTGAAAGCCTCGTACCCTGG HPRT1 (GenBank Accession No.NM_000194 (SEQ ID NO: 379), HPRT1 Forward primer (SEQ ID NO: 560):TGACACTGGCAAAACAATGCA HPRT1 Reverse primer (SEQ ID NO: 561):GGTCCTTTTCACCAGCAAGCT HPRT1-amplicon (SEQ ID NO: 380):TGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACC G6PD (GenBank Accession No.NM_000402 (SEQ ID NO: 405)) G6PDForward primer (SEQ ID NO: 564):gaggccgtcaccaagaacat G6PD Reverse primer (SEQ ID NO: 565):ggacagccggtcagagctc G6PD-amplicon (SEQ ID NO: 404):gaggccgtcaccaagaacattcacgagtcctgcatgagccagataggctggaaccgcatcatcgtggagaagcccttcgggagggacctgcagagctctg accggctgtcc RPS27A(GenBank Accession No. NM_002954 (SEQ ID NO:403),) RPS27A Forward primer(SEQ ID NO: 566): CTGGCAAGCAGCTGGAAGAT RPS27A Reverse primer (SEQ ID NO:567): TTCTTAGCACCACCACGAAGTC RPS27A-amplicon (SEQ ID NO: 402):CTGGCAAGCAGCTGGAAGATGGACGTACTTTGTCTGACTACAATATTCAAAAGGAGTCTACTCTTCATCTTGTGTTGAGACTTCGTGGTGGTGCTAAGAA A

The sequences of the housekeeping genes measured in all the examples inthe lung panel were as follows:

Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366),) UbiquitinForward primer (SEQ ID NO: 568): ATTTGGGTCGCGGTTCTTG Ubiquitin Reverseprimer (SEQ ID NO: 569): TGCCTTGACATTCTCGATGGT Ubiquitin-amplicon (SEQID NO: 367): ATTTGGGTCGCGGTTCTTGTTTGTGGATCGCTGTGATCGTCACTTGACAATGCAGATCTTCGTGAAGACTCTGACTGGTAAGACCATCACCCTCGAGGTTGAGCCCAGTGACACCATCGAGAATGTCAAGGCA SDHA (GenBank Accession No. NM_004168(SEQ ID NO: 364),) SDHA Forward primer (SEQ ID NO: 556):TGGGAACAAGAGGGCATCTG SDHA Reverse primer (SEQ ID NO: 557):CCACCACTGCATCAAATTCATG SDHA-amplicon (SEQ ID NO: 365):TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCAGTAGTGGATCATGAATTTGATGCAGTGGTGG PBGD (GenBank Accession No.BC019323 (SEQ ID NO: 381)), PBGD Forward primer (SEQ ID NO: 558):TGAGAGTGATTCGCGTGGG PBGD Reverse primer (SEQ ID NO: 559):CCAGGGTACGAGGCTTTCAAT PBGD-amplicon (SEQ ID NO: 382):TGAGAGTGATTCGCGTGGGTACCCGCAAGAGCCAGCTTGCTCGCATACAGACGGACAGTGTGGTGGCAACATTGAAAGCCTCGTACCCTGG HPRT1 (GenBank Accession No.NM_000194 (SEQ ID NO: 379)), HPRT1 Forward primer (SEQ ID NO: 560):TGACACTGGCAAAACAATGCA HPRT1 Reverse primer (SEQ ID NO: 561):GGTCCTTTTCACCAGCAAGCT HPRT1-amplicon (SEQ ID NO: 380):TGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACC

The sequences of the housekeeping genes measured in all the examples onbreast cancer panel were as follows:

G6PD (GenBank Accession No. NM_000402 (SEQ ID NO: 405)) G6PD Forwardprimer (SEQ ID NO: 564): gaggccgtcaccaagaacat G6PD Reverse primer (SEQID NO: 565): ggacagccggtcagagctc G6PD-amplicon (SEQ ID NO: 404):gaggccgtcaccaagaacattcacgagtcctgcatgagccagataggctggaaccgcatcatcgtggagaagcccttcgggagggacctgcagagctctg accggctgtcc SDHA(GenBank Accession No. NM_004168 (SEQ ID NO: 364),) SDHA Forward primer(SEQ ID NO: 556): TGGGAACAAGAGGGCATCTG SDHA Reverse primer (SEQ ID NO:557): CCACCACTGCATCAAATTCATG SDHA-amplicon (SEQ ID NO: 365):TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCAGTAGTGGATCATGAATTTGATGCAGTGGTGG PBGD (GenBank Accession No.BC019323 (SEQ ID NO: 381)), PBGD Forward primer (SEQ ID NO: 558):TGAGAGTGATTCGCGTGGG PBGD Reverse primer (SEQ ID NO: 559):CCAGGGTACGAGGCTTTCAAT PBGD-amplicon (SEQ ID NO: 382):TGAGAGTGATTCGCGTGGGTACCCGCAAGAGCCAGCTTGCTCGCATACAGACGGACAGTGTGGTGGCAACATTGAAAGCCTCGTACCCTGG HPRT1 (GenBank Accession No.NM_000194 (SEQ ID NO: 379), HPRT1 Forward primer (SEQ ID NO: 560):TGACACTGGCAAAACAATGCA HPRT1 Reverse primer (SEQ ID NO: 561):GGTCCTTTTCACCAGCAAGCT HPRT1-amplicon (SEQ ID NO: 380):TGACACTGGCAAAACAATGCAGACTTTGCTTTCCTTGGTCAGGCAGTATAATCCAAAGATGGTCAAGGTCGCAAGCTTGCTGGTGAAAAGGACC

The sequences of the housekeeping genes measured in all the examples onnormal tissue samples panel were as follows:

RPL19 (GenBank Accession No. NM_000981 (SEQ ID NO: 369)) RPL19Forwardprimer (SEQ ID NO: 570): TGGCAAGAAGAAGGTCTGGTTAG RPL19Reverse primer(SEQ ID NO: 571): TGATCAGCCCATCTTTGATGAG RPL19-amplicon (SEQ ID NO:368): TGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATGCCAACTCCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATC A TATAbox (GenBankAccession No. NM_003194 (SEQ ID NO:371)), TATA box Forward primer (SEQID NO: 572): CGGTTTGCTGCGGTAATCAT TATA box Reverse primer (SEQ ID NO:573): TTTCTTGCTGCCAGTCTGGAC TATA (SEQ ID NO:370) box amplicon:CGGTTTGCTGCGGTAATCATGAGGATAAGAGAGCCACGAACCACGGCACTGATTTTCAGTTCTGGGAAAATGGTGTGCACAGGAGCCAAGAGTGAAGAACAGTCCAGACTGGCAGCAAGAAA Ubiquitin (GenBank Accession No. BC000449 (SEQ IDNO:366)) Ubiquitin Forward primer (SEQ ID NO: 568): ATTTGGGTCGCGGTTCTTGUbiquitin Reverse primer (SEQ ID NO: 569): TGCCTTGACATTCTCGATGGTUbiquitin-amplicon (SEQ ID NO: 367):ATTTGGGTCGCGGTTCTTGTTTGTGGATCGCTGTGATCGTCACTTGACAATGCAGATCTTCGTGAAGACTCTGACTGGTAAGACCATCACCCTCGAGGTTGAGCCCAGTGACACCATCGAGAATGTCAAGGCA SDHA (GenBank Accession No. NM_004168(SEQ ID NO: 364),) SDHA Forward primer (SEQ ID NO: 556):TGGGAACAAGAGGGCATCTG SDHA Reverse primer (SEQ ID NO: 557):CCACCACTGCATCAAATTCATG SDHA-amplicon (SEQ ID NO: 365):TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCAGTAGTGGATCATGAATTTGATGCAGTGGTGG

Cluster HSFLT

Cluster HSFLT features at least 15 transcript(s) and at least 58segment(s) of interest, the names for which are described in Tables 6and 7, respectively and certain protein variants are described in table8.

TABLE 6 Transcripts Transcript Name HSFLT_T7 (SEQ ID NO: 1) HSFLT_T8(SEQ ID NO: 2) HSFLT_T9 (SEQ ID NO: 3) HSFLT_T10 (SEQ ID NO: 4)HSFLT_T13 (SEQ ID NO: 5) HSFLT_T14 (SEQ ID NO: 6) HSFLT_T17 (SEQ ID NO:7) HSFLT_T19 (SEQ ID NO: 8) HSFLT_T20 (SEQ ID NO: 9) HSFLT_T21 (SEQ IDNO: 10) HSFLT_T22 (SEQ ID NO: 11) HSFLT_T23 (SEQ ID NO: 12) HSFLT_T24(SEQ ID NO: 13) HSFLT_T25 (SEQ ID NO: 14) HSFLT_T26 (SEQ ID NO: 15)

TABLE 7 Segments Segment Name HSFLT_N0 (SEQ ID NO: 32) HSFLT_N5 (SEQ IDNO: 33) HSFLT_N6 (SEQ ID NO: 34) HSFLT_N8 (SEQ ID NO: 35) HSFLT_N9 (SEQID NO: 36) HSFLT_N11 (SEQ ID NO: 37) HSFLT_N14 (SEQ ID NO: 38) HSFLT_N15(SEQ ID NO: 39) HSFLT_N17 (SEQ ID NO: 40) HSFLT_N19 (SEQ ID NO: 41)HSFLT_N20 (SEQ ID NO: 42) HSFLT_N24 (SEQ ID NO: 43) HSFLT_N26 (SEQ IDNO: 44) HSFLT_N30 (SEQ ID NO: 45) HSFLT_N38 (SEQ ID NO: 46) HSFLT_N41(SEQ ID NO: 47) HSFLT_N42 (SEQ ID NO: 48) HSFLT_N44 (SEQ ID NO: 49)HSFLT_N46 (SEQ ID NO: 50) HSFLT_N48 (SEQ ID NO: 51) HSFLT_N52 (SEQ IDNO: 52) HSFLT_N59 (SEQ ID NO: 53) HSFLT_N63 (SEQ ID NO: 54) HSFLT_N68(SEQ ID NO: 55) HSFLT_N74 (SEQ ID NO: 56) HSFLT_N82 (SEQ ID NO: 57)HSFLT_N93 (SEQ ID NO: 58) HSFLT_N98 (SEQ ID NO: 59) HSFLT_N100 (SEQ IDNO: 60) HSFLT_N103 (SEQ ID NO: 530) HSFLT_N3 (SEQ ID NO: 502) HSFLT_N22(SEQ ID NO: 503) HSFLT_N28 (SEQ ID NO: 504) HSFLT_N32 (SEQ ID NO: 505)HSFLT_N34 (SEQ ID NO: 506) HSFLT_N36 (SEQ ID NO: 507) HSFLT_N50 (SEQ IDNO: 508) HSFLT_N55 (SEQ ID NO: 509) HSFLT_N57 (SEQ ID NO: 510) HSFLT_N61(SEQ ID NO: 511) HSFLT_N65 (SEQ ID NO: 512) HSFLT_N66 (SEQ ID NO: 513)HSFLT_N70 (SEQ ID NO: 514) HSFLT_N72 (SEQ ID NO: 515) HSFLT_N75 (SEQ IDNO: 516) HSFLT_N77 (SEQ ID NO: 517) HSFLT_N78 (SEQ ID NO: 518) HSFLT_N79(SEQ ID NO: 519) HSFLT_N84 (SEQ ID NO: 520) HSFLT_N88 (SEQ ID NO: 521)HSFLT_N91 (SEQ ID NO: 522) HSFLT_N92 (SEQ ID NO: 523) HSFLT_N94 (SEQ IDNO: 524) HSFLT_N95 (SEQ ID NO: 525) HSFLT_N97 (SEQ ID NO: 526) HSFLT_N99(SEQ ID NO: 527) HSFLT_N101 (SEQ ID NO: 528) HSFLT_N102 (SEQ ID NO: 529)

TABLE 8 Proteins and their Corresponding Transcript Descriptions:Protein Name Corresponding Transcript(s) HSFLT_P6 (SEQ ID NO: 16)HSFLT_T9 (SEQ ID NO: 3) HSFLT_P7 (SEQ ID NO: 17) HSFLT_T10 (SEQ ID NO:4) HSFLT_P10 (SEQ ID NO: 18) HSFLT_T13 (SEQ ID NO: 5) HSFLT_P11 (SEQ IDNO: 19) HSFLT_T14 (SEQ ID NO: 6) HSFLT_P13 (SEQ ID NO: 20) HSFLT_T17(SEQ ID NO: 7) HSFLT_P14 (SEQ ID NO: 21) HSFLT_T19 (SEQ ID NO: 8)HSFLT_P15 (SEQ ID NO: 22) HSFLT_T20 (SEQ ID NO: 9) HSFLT_P16 (SEQ ID NO:23) HSFLT_T21 (SEQ ID NO: 10) HSFLT_P17 (SEQ ID NO: 24) HSFLT_T22 (SEQID NO: 11) HSFLT_P18 (SEQ ID NO: 25) HSFLT_T23 (SEQ ID NO: 12) HSFLT_P19(SEQ ID NO: 26) HSFLT_T24 (SEQ ID NO: 13) HSFLT_P20 (SEQ ID NO: 27)HSFLT_T25 (SEQ ID NO: 14) HSFLT_P21 (SEQ ID NO: 28) HSFLT_T26 (SEQ IDNO: 15) HSFLT_P41 (SEQ ID NO: 29) HSFLT_T21 (SEQ ID NO: 10) HSFLT_P48(SEQ ID NO: 30) HSFLT_T7 (SEQ ID NO: 1) HSFLT_P49 (SEQ ID NO: 31)HSFLT_T8 (SEQ ID NO: 2)

The sequences listed in Tables 8 comprise variants of the known proteinVascular endothelial growth factor receptor 1 precursor (SwissProtaccession identifier VGR1_HUMAN (SEQ ID NO: 359); known also accordingto the synonyms EC 2.7.1.112; VEGFR-1; Vascular permeability factorreceptor; Tyrosine-protein kinase receptor FLT; Flt-1; Tyrosine-proteinkinase FRT; Fms-like tyrosine kinase 1)), and may be referred to hereinas “the corresponding native protein”.

Protein Vascular endothelial growth factor receptor 1 precursor isassociated with the following function(s): it is a receptor for VEGF,VEGFB and PGF, has tyrosine-protein kinase activity. The VEGF-kinaseligand/receptor signaling system plays a key role in vasculardevelopment and regulation of vascular permeability. Isoform SFlt1 mayhave an inhibitory role in angiogenesis. The sequence for proteinVascular endothelial growth factor receptor 1 precursor is given at theend of the application, as “Vascular endothelial growth factor receptor1 precursor amino acid sequence”. Known polymorphisms for this sequenceinclude an SNP at amino acid position 779, having an L to Fsubstitution.

According to this aspect of the invention and in some embodiments, thepolypeptides related thereto, and polynucleotides encoding the same, maybe useful in applications in the following: angiogenesis inhibition;angiogenesis stimulation; endothelial growth factor agonism; endothelialgrowth factor receptor kinase inhibition, or combinations thereof.

In some embodiments, related polypeptides/polynucleotides of thisinvention will accordingly have the following therapeutic indication:anticancer, cardiovascular; growth stimulation; antidiabetic; vulnerary,or others.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: positive regulation of cellproliferation; pregnancy; transmembrane receptor protein tyrosine kinasesignaling pathway, which are annotation(s) related to BiologicalProcess; receptor activity; vascular endothelial growth factor receptoractivity, which are annotation(s) related to Molecular Function; andextracellular space; integral to plasma membrane, which areannotation(s) related to Cellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

According to some embodiments of the present invention, variants of thiscluster according to the present invention (amino acid and/or nucleicacid sequences of HSFLT) may optionally have one or more of thefollowing utilities, as described below. It should be noted that theseutilities are optionally and preferably suitable for human and non-humananimals as subjects, except where otherwise noted.

A non-limiting example of such a diagnostic utility is detection ofvarious cancer tumors. Vascular endothelial growth factor (VEGF) levelsare associated with increased angiogenesis and aggressive tumor growth.In addition, it may serve as a marker for the early detection ofcoronary artery disease (CAD): experimental data show abnormalangiogenesis (VEGF and sFlt-1) in the patients with CAD.

Placental Growth Factor (HSPLGF), a member of the vascular endothelialgrowth factor (VEGF) family, competes with VEGF for binding to VEGFReceptor-1 (VEGFR1) (Am J Physiol Heart Circ Physiol. Apr. 24, 2003).Another non-limiting example of diagnostic utility of one or more HSFLTvariants according to the present invention may optionally be related toone or more of the utilities of the HSPLGF placental growth factor,described herein (see the “Table of Utilities for Variants of HSPLGF,related to placental growth factor”, herein). Therefore, variants ofHSFLT cluster according to the present invention (amino acid and/ornucleic acid sequences of HSFLT) could be used as molecular marker forconditions including but not limited to the following: inflammation,pathological angiogenesis, monocyte recruitment that underlie chronicinflammatory disease.

Another non-limiting example of the utility of the variants of HSFLTcluster according to the present invention (amino acid and/or nucleicacid sequences of HSFLT) is using this marker as a surrogate marker fordetermining the efficacy of treatment for modulators, preferablyinhibitors, of the VEGF-kinase ligand/receptor signaling system, whichplays a key role in vascular development and regulation of vascularpermeability. Blocking this system may be used to block angiogenesis,for example for treating cancer. The system may also optionally bemodulated for treating cardiovascular conditions, peripheral vasculardisease; ulcers; and ischaemia. This marker could also be used as asurrogate marker for determining the efficacy of treatment formodulators of the above conditions. Its suitability for treatment of theabove conditions was described in PCT Application No. WO 05/072340 andhence is presence is clearly related to the mechanism of action of theabove system in the body.

As noted above, cluster HSFLT features 15 transcript(s), which werelisted in Table 6 above. These transcript(s) encode for protein(s) whichare variant(s) of protein Vascular endothelial growth factor receptor 1precursor. A description of each variant protein according to thepresent invention is provided as follows:

Variant protein HSFLT_P6 (SEQ ID NO:16) according to the presentinvention has an amino acid sequence as provided in the sequencelisting; and is encoded by transcript(s) HSFLT_T9 (SEQ ID NO:3). Analignment is provided with respect to the known protein (Vascularendothelial growth factor receptor 1 precursor) in the alignment tableon the attached CD-ROM.

A brief description of the relationship of the variant protein accordingto the present invention to each such aligned protein is as follows:

1. Comparison Report Between HSFLT_P6 (SEQ ID NO:16) and VGR1_HUMAN_V1(SEQ ID NO: 575):

A. An isolated chimeric polypeptide as set forth in HSFLT_P6 (SEQ IDNO:16), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MTAP (SEQ ID NO: 459) corresponding to amino acids1-4 of HSFLT_P6 (SEQ ID NO:16), and a second amino acid sequence beingat least 90% homologous toFPLDTNIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMPRAPEYSTPEIYQIMLDCWBRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI corresponding to aminoacids 172-1338 of VGR1_HUMAN_V1 (SEQ ID NO: 575), which also correspondsto amino acids 5-1171 of HSFLT_P6 (SEQ ID NO:16), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P6 (SEQ IDNO:16), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMTAP (SEQ ID NO: 459) of HSFLT_P6 (SEQ ID NO:16).

It should be noted that the known protein sequences VGR1_HUMAN (SEQ IDNO: 359) and NP_(—)002010 (SEQ ID NO: 531) have one or more changes thanthe sequence for VGR1_HUMAN_V1 (SEQ ID NO: 575). These changes werepreviously known to occur and are listed in table 9.

TABLE 9 Changes to VGR1_HUMAN_V1 (SEQ ID NO: 575) SNP position on aminoacid sequence Type of change 779 conflict

3. Comparison Report Between HSFLT_P6 (SEQ ID NO:16) and P17948-2 (SEQID NO:360)

A. An isolated chimeric polypeptide as set forth in HSFLT_P6 (SEQ IDNO:16), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MTAP (SEQ ID NO: 459) corresponding to amino acids1-4 of HSFLT_P6 (SEQ ID NO:16), a second amino acid sequence being atleast 90% homologous toFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGBLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNBNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIR corresponding to amino acids 172-656of P17948-2 (SEQ ID NO:360), which also corresponds to amino acids 5-489of HSFLT_P6 (SEQ ID NO:16), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) corresponding to amino acids 490-1171 ofHSFLT_P6 (SEQ ID NO:16), wherein said first amino acid sequence, secondamino acid sequence and third amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P6 (SEQ IDNO:16), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMTAP (SEQ ID NO: 459) of HSFLT_P6 (SEQ ID NO:16).

C. An isolated polypeptide encoding for an edge portion of HSFLT_P6 (SEQID NO:16), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence DQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNBQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIMHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) of HSFLT_P6 (SEQ ID NO:16).

The location of the variant protein was determined via the use of anumber of different software programs and analyses, as described andincluding analyses from SignalP and other specialized programs.

In some embodiments of the invention, the variant protein is located inor in association with the cell membrane.

Variant protein HSFLT_P6 (SEQ ID NO:16) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 10,(lists the position(s) within the sequence and the alternative aminoacid(s); the presence of known SNPs in variant protein HSFLT_P6 (SEQ IDNO:16) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 10 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 83 L -> P 117 Q -> R 176 V -> A 227 D -> G 593I -> V 680 F -> S

The glycosylation sites of variant protein HSFLT_P6 (SEQ ID NO:16), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 11 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 11 Glycosylation site(s) Position(s) on known Position(s) on aminoacid sequence Present in variant protein? variant protein 29 Yes 29 84Yes 84 100 No 156 Yes 156 164 No 235 Yes 235 250 Yes 250 307 Yes 307 380Yes 380 430 Yes 430 453 Yes 453 458 Yes 458 499 Yes 499

The phosphorylation sites of variant protein HSFLT_P6 (SEQ ID NO:16), ascompared to the known protein, are described in Table 12 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 12 Phosphorylation site(s) Position(s) on known amino Position(s)on acid sequence Present in variant protein? variant protein 886 Yes 8861002 Yes 1002 1046 Yes 1046 1075 Yes 1075 1160 Yes 1160 1166 Yes 1166

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 13:

TABLE 13 InterPro domain(s) Domain description Analysis type Position(s)on protein Protein kinase BlastProDom 661-760, 826-992 Vascularendothelial growth FPrintScan 17-27, 75-87, 223-240, factor receptor,VEGFR 281-295 Vascular endothelial growth FPrintScan 57-80, 106-123,183-203, factor receptor 1, VEGFR1 208-222 Immunoglobulin-like HMMPfam78-146, 403-471, 508-566 Protein kinase HMMPfam 660-987 Tyrosine proteinkinase HMMSmart 660-987 Serine HMMSmart 660-991 Immunoglobulin V-typeHMMSmart 80-146, 405-471 Immunoglobulin C2 type HMMSmart 76-151,181-245, 401-476, 506-571 Immunoglobulin subtype HMMSmart 70-162,177-258, 272-386, 395-491, 500-582 Protein kinase ProfileScan 660-991Immunoglobulin-like ProfileScan 63-160, 182-237, 261-386, 389-487,494-580 Protein kinase ScanRegExp 666-694 Tyrosine protein kinase,ScanRegExp 851-863 active site Receptor tyrosine kinase, ScanRegExp719-732 class III

Variant protein HSFLT_P6 (SEQ ID NO:16) is encoded by the followingtranscript(s): HSFLT_T9 (SEQ ID NO:3), for which the coding portionbegins at position 1113 and ends at position 4625. The transcript alsohas the following SNPs as listed in Table 14 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the last column indicates whether the SNP is known or not; thepresence of known SNPs in variant protein HSFLT_P6 (SEQ ID NO:16)sequence provides support for the deduced sequence of this variantprotein according to the present invention).

TABLE 14 Nucleic acid SNPs Polymorphism: Position(s) on nucleotidesequence T -> C 1360; 1639; 3151; 3815; 4250 A -> G 1462; 1622; 1792;2889; 3683; 5718; 7237 T -> G 6143; 6148; 7266 C -> T 1830; 4975 G -> A2315 C -> A 3362 T -> 4774 G -> T 5896 A -> C 6984

In one embodiment, a variant protein HSFLT_P7 according to the presentinvention has an amino acid sequence as set forth in (SEQ ID NO:17). Inone embodiment, it is encoded by a p HSFLT_T10 polynucleotide (SEQ IDNO:4), and an alignment of the variant to the known protein (Vascularendothelial growth factor receptor 1 precursor) is presented in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HSFLT_P7 (SEQ ID NO:17) and VGR1_HUMAN_V1(SEQ ID NO: 575):

A. An isolated chimeric polypeptide as set forth in HSFLT_P7 (SEQ IDNO:17), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPLPFQ (SEQ ID NO: 576) corresponding to amino acids1-6 of HSFLT_P7 (SEQ ID NO:17), and a second amino acid sequence beingat least 90% homologous toFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGBLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMUVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWBRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI corresponding to aminoacids 172-1338 of VGR1_HUMAN_V1 (SEQ ID NO: 575), which also correspondsto amino acids 7-1173 of HSFLT_P7 (SEQ ID NO:17), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P7 (SEQ IDNO:17), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMPLPFQ (SEQ ID NO: 576) of HSFLT_P7 (SEQ ID NO:17).

2. Comparison Report Between HSFLT_P7 (SEQ ID NO:17) and NP_(—)002010_V1(SEQ ID NO: 574):

A. An isolated chimeric polypeptide as set forth in HSFLT_P7 (SEQ IDNO:17), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPLPFQ (SEQ ID NO: 576) corresponding to amino acids1-6 of HSFLT_P7 (SEQ ID NO:17), and a second amino acid sequence beingat least 90% homologous toFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHBLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKBPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI corresponding to aminoacids 172-1338 of NP_(—)002010_V1 (SEQ ID NO: 574), which alsocorresponds to amino acids 7-1173 of HSFLT_P7 (SEQ ID NO:17), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P7 (SEQ IDNO:17), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMPLPFQ (SEQ ID NO: 576) of HSFLT_P7 (SEQ ID NO:17).

3. Comparison Report Between HSFLT_P7 (SEQ ID NO:17) and P17948-2 (SEQID NO:360)

A. An isolated chimeric polypeptide as set forth in HSFLT_P7 (SEQ IDNO:17), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPLPFQ (SEQ ID NO: 576) corresponding to amino acids1-6 of HSFLT_P7 (SEQ ID NO:17), a second amino acid sequence being atleast 90% homologous toFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIR corresponding to amino acids 172-656of P17948-2 (SEQ ID NO:360), which also corresponds to amino acids 7-491of HSFLT_P7 (SEQ ID NO:17), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) corresponding to amino acids 492-1173 ofHSFLT_P7 (SEQ ID NO:17), wherein said first amino acid sequence, secondamino acid sequence and third amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P7 (SEQ IDNO:17), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMPLPFQ (SEQ ID NO: 576) of HSFLT_P7 (SEQ ID NO:17).

C. An isolated polypeptide encoding for an edge portion of HSFLT_P7 (SEQID NO:17), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNMIQQEPGIILGPGSSTLFIERVTEEDEGVYHCKATNQKGSVESSAYLTVQGTSDKSNLELITLTCTCVAATLFWLLLTLFIRKMKRSSSEIKTDYLSIIMDPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTVAVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI (SEQ ID NO: 460) of HSFLT_P7 (SEQ ID NO:17).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is membrane.

Variant protein HSFLT_P7 (SEQ ID NO:17) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 15,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P7 (SEQ ID NO:17) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 15 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 85 L -> P 119 Q -> R 178 V -> A 229 D -> G 595I -> V 682 F -> S

The glycosylation sites of variant protein HSFLT_P7 (SEQ ID NO:17), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 16 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 16 Glycosylation site(s) Position(s) on known amino Position(s) onacid sequence Present in variant protein? variant protein 31 Yes 31 86Yes 86 100 No 158 Yes 158 164 No 237 Yes 237 252 Yes 252 309 Yes 309 382Yes 382 432 Yes 432 455 Yes 455 460 Yes 460 501 Yes 501

The phosphorylation sites of variant protein HSFLT_P7 (SEQ ID NO:17), ascompared to the known protein, are described in Table 17 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 17 Phosphorylation site(s) Position(s) on known amino Position(s)on acid sequence Present in variant protein? variant protein 888 Yes 8881004 Yes 1004 1048 Yes 1048 1077 Yes 1077 1162 Yes 1162 1168 Yes 1168

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 18:

TABLE 18 InterPro domain(s) Domain description Analysis type Position(s)on protein Protein kinase BlastProDom 663-762, 828-994 Vascularendothelial growth factor FPrintScan 19-29, 77-89, 225-242, 283-297receptor, VEGFR Vascular endothelial growth factor FPrintScan 59-82,108-125, 185-205, 210-224 receptor 1, VEGFR1 Immunoglobulin-like HMMPfam80-148, 405-473, 510-568 Protein kinase HMMPfam 662-989 Tyrosine proteinkinase HMMSmart 662-989 Serine HMMSmart 662-993 Immunoglobulin V-typeHMMSmart 82-148, 407-473 Immunoglobulin C2 type HMMSmart 78-153,183-247, 403-478, 508-573 Immunoglobulin subtype HMMSmart 72-164,179-260, 274-388, 397-493, 502-584 Protein kinase ProfileScan 662-993Immunoglobulin-like ProfileScan 65-162, 184-239, 263-388, 391-489,496-582 Protein kinase ScanRegExp 668-696 Tyrosine protein kinase,active site ScanRegExp 853-865 Receptor tyrosine kinase, class IIIScanRegExp 721-734

Variant protein HSFLT_P7 (SEQ ID NO:17) is encoded by the followingtranscript(s): HSFLT_T10 (SEQ ID NO:4), for which the coding portionbegins at position 448 and ends at position 3966. The transcript alsohas the following SNPs as listed in Table 19 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P7 (SEQ IDNO:17) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 19 Nucleic acid SNPs Polymorphism nucleotide position T -> C 701,980, 2492, 3156, 3591 A -> G 803, 963, 1133, 2230, 3024, 5059, 6578 T ->G 5484, 5489, 6607 C -> T 1171, 4316 G -> A 1656 C -> A 2703 G -> T 5237A -> C 6325 T -> 4115

In some embodiments, HSFLT_P10 of the present invention has an aminoacid sequence homologous to or as set forth in SEQ ID NO:18, and may beencoded by transcript(s) HSFLT_T13 (SEQ ID NO:5). An alignment ofHSFLT_P10 to known protein vascular endothelial growth factor receptor 1precursor is provided in the alignment table on the attached CD-ROM. Abrief description of the relationship of the variant protein accordingto the present invention to each such aligned protein is as follows:

1. Comparison report between HSFLT_P10 (SEQ ID NO:18) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P10 (SEQ IDNO:18), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEP corresponding to amino acids 1-705 ofVGR1_HUMAN (SEQ ID NO: 359), which also corresponds to amino acids 1-705of HSFLT_P10 (SEQ ID NO:18), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO:462) corresponding to amino acids 706-733 of HSFLT_P10 (SEQ ID NO:18),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P10(SEQ ID NO:18), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO: 462)of HSFLT_P10 (SEQ ID NO:18).

2. Comparison Report Between HSFLT_P10 (SEQ ID NO:18) and P17948-2 (SEQID NO:360)

A. An isolated chimeric polypeptide as set forth in HSFLT_P10 (SEQ IDNO:18), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFHSNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIR correspondingto amino acids 1-656 of P17948-2 (SEQ ID NO:360), which also correspondsto amino acids 1-656 of HSFLT_P10 (SEQ ID NO:18), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPELYTSTSPSSSSSSPLSSSSSSSSSSSS(SEQ ID NO: 463) corresponding to amino acids 657-733 of HSFLT_P10 (SEQID NO:18), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P10(SEQ ID NO:18), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPELYTSTSPSSSSSSPLSSSSSSSSSSSS(SEQ ID NO: 463) of HSFLT_P10 (SEQ ID NO:18).

3. Comparison Report Between HSFLT_P10 (SEQ ID NO:18) and NP_(—)002010(SEQ ID NO: 531):

A. An isolated chimeric polypeptide as set forth in HSFLT_P10 (SEQ IDNO:18), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEP corresponding to amino acids 1-705 ofNP_(—)002010 (SEQ ID NO: 531), which also corresponds to amino acids1-705 of HSFLT_P10 (SEQ ID NO:18), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQID NO: 462) corresponding to amino acids 706-733 of HSFLT_P10 (SEQ IDNO:18), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P10(SEQ ID NO:18), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence ELYTSTSPSSSSSSPLSSSSSSSSSSSS (SEQ ID NO: 462)of HSFLT_P10 (SEQ ID NO:18).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P10 (SEQ ID NO:18) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 20,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P10 (SEQ ID NO:18) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 20 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P10 (SEQ ID NO:18), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 21 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 21 Glycosylation site(s) Position(s) on known Position(s) on aminoacid sequence Present in variant protein? variant protein 100 Yes 100164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417 Yes 417474 Yes 474 547 Yes 547 597 Yes 597 620 Yes 620 625 Yes 625 666 Yes 666

The phosphorylation sites of variant protein HSFLT_P10 (SEQ ID NO:18),as compared to the known protein, are described in Table 22 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 22 Phosphorylation site(s) Position(s) on known Position(s) onamino acid sequence Present in variant protein? variant protein 1053 No1169 No 1213 No 1242 No 1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 23:

TABLE 23 InterPro domain(s) Domain description Analysis type Position(s)on protein Vascular endothelial growth factor FPrintScan 89-107,125-136, 184-194, 242-254, 390-407, receptor, VEGFR 448-462 Vascularendothelial growth factor FPrintScan 26-41, 79-93, 130-155, 224-247,273-290, receptor 1, VEGFR1 350-370, 375-389 Immunoglobulin-like HMMPfam245-313, 570-638, 675-731 Immunoglobulin V-type HMMSmart 247-313,572-638 Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412,568-643, 673-732 Immunoglobulin subtype HMMSmart 38-129, 143-224,237-329, 344-425, 439-553, 562-658 Immunoglobulin-like ProfileScan32-107, 230-327, 349-404, 428-553, 556-654, 661-733

Variant protein HSFLT_P1 (SEQ ID NO:18) is encoded by the followingtranscript(s): HSFLT_T13 (SEQ ID NO:5), for which the coding portionstarts at position 315 and ends at position 2513. The transcript alsohas the following SNPs as listed in Table 24 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P10 (SEQ IDNO:18) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 24 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence -> C  823 T -> C 1063, 1342 A -> G 1165, 1325, 1495 C -> T 1533G -> A 2018 G -> T 3301

Variant protein HSFLT_P11 (SEQ ID NO:19) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T14 (SEQ ID NO:6). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P11 (SEQ ID NO:19) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in a chimeric HSFLT_P11(SEQ ID NO:19) polypeptide comprising a first amino acid sequence beingat least 90% homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEWWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPG corresponding to amino acids 1-706 ofVGR1_HUMAN (SEQ ID NO: 359), which also corresponds to amino acids 1-706of HSFLT_P11 (SEQ ID NO:19), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence SANTAVNKKTEI (SEQ ID NO: 464)corresponding to amino acids 707-718 of HSFLT_P11 (SEQ ID NO:19),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P11(SEQ ID NO:19), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence SANTAVNKKTEI (SEQ ID NO: 464) of HSFLT_P11(SEQ ID NO:19).

2. Comparison Report Between HSFLT_P11 (SEQ ID NO:19) and P17948-2 (SEQID NO:360)

A. An isolated chimeric polypeptide as set forth in HSFLT_P11 (SEQ IDNO:19), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEWWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIR correspondingto amino acids 1-656 of P17948-2 (SEQ ID NO:360), which also correspondsto amino acids 1-656 of HSFLT_P11 (SEQ ID NO:19), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGSANTAVNKKTEI (SEQ IDNO: 465) corresponding to amino acids 657-718 of HSFLT_P11 (SEQ IDNO:19), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P11(SEQ ID NO:19), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGSANTAVNKKTEI (SEQ IDNO: 465) of HSFLT_P11 (SEQ ID NO:19).

3. Comparison Report Between HSFLT_P11 (SEQ ID NO:19) and NP_(—)002010(SEQ ID NO: 531):

A. An isolated chimeric polypeptide as set forth in HSFLT_P11 (SEQ IDNO:19), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPG corresponding to amino acids 1-706 ofNP_(—)002010 (SEQ ID NO: 531), which also corresponds to amino acids1-706 of HSFLT_P11 (SEQ ID NO:19), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence SANTAVNKKTEI (SEQ ID NO: 464)corresponding to amino acids 707-718 of HSFLT_P11 (SEQ ID NO:19),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P11(SEQ ID NO:19), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence SANTAVNKKTEI (SEQ ID NO: 464) of HSFLT_P11(SEQ ID NO:19).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P11 (SEQ ID NO:19) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 25,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P11 (SEQ ID NO:19) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 25 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P11 (SEQ ID NO:19), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 26 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 26 Glycosylation site(s) Position(s) on known Position(s) on aminoacid sequence Present in variant protein? variant protein 100 Yes 100164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417 Yes 417474 Yes 474 547 Yes 547 597 Yes 597 620 Yes 620 625 Yes 625 666 Yes 666

The phosphorylation sites of variant protein HSFLT_P11 (SEQ ID NO:19),as compared to the known protein, are described in Table 27 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 27 Phosphorylation site(s) Position(s) on known amino acidsequence Present in variant protein? 1053 No 1169 No 1213 No 1242 No1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 28:

TABLE 28 InterPro domain(s) Domain description Analysis type Position(s)on protein Vascular endothelial growth factor FPrintScan 89-107,125-136, 184-194, 242-254, 390-407, receptor, VEGFR 448-462 Vascularendothelial growth factor FPrintScan 26-41, 79-93, 130-155, 224-247,273-290, receptor 1, VEGFR1 350-370, 375-389 Immunoglobulin-like HMMPfam245-313, 570-638 Immunoglobulin V-type HMMSmart 247-313, 572-638Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412, 568-643,673-716 Immunoglobulin subtype HMMSmart 38-129, 143-224, 237-329,344-425, 439-553, 562-658 Immunoglobulin-like ProfileScan 32-107,230-327, 349-404, 428-553, 556-654, 661-718

Variant protein HSFLT_P11 (SEQ ID NO:19) is encoded by the followingtranscript(s): HSFLT_T14 (SEQ ID NO:6), for which the coding portionstarts at position 315 and ends at position 2468. The transcript alsohas the following SNPs as listed in Table 29 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P11 (SEQ IDNO:19) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 29 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence -> C  823 T -> C 1063, 1342 A -> G 1165, 1325, 1496 C -> T 1533G -> A 2018

Variant protein HSFLT_P13 (SEQ ID NO:20) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T17 (SEQ ID NO:7). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P13 (SEQ ID NO:20) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P13 (SEQ IDNO:20), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPG corresponding to amino acids 1-706 ofVGR1_HUMAN (SEQ ID NO: 359), which also corresponds to amino acids 1-706of HSFLT_P13 (SEQ ID NO:20), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ IDNO: 466) corresponding to amino acids 707-736 of HSFLT_P13 (SEQ IDNO:20), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P13(SEQ ID NO:20), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO:466) of HSFLT_P13 (SEQ ID NO:20).

2. Comparison Report Between HSFLT_P13 (SEQ ID NO:20) and P17948-2 (SEQID NO:360):

A. An isolated chimeric polypeptide as set forth in HSFLT_P13 (SEQ IDNO:20), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHBINQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIR correspondingto amino acids 1-656 of P17948-2 (SEQ ID NO:360), which also correspondsto amino acids 1-656 of HSFLT_P13 (SEQ ID NO:20), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNEKIQQEPGKRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO: 467) corresponding to amino acids 657-736 of HSFLT_P13(SEQ ID NO:20), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P13(SEQ ID NO:20), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNHKIQQEPGKRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO: 467) of HSFLT_P13 (SEQ ID NO:20).

3. Comparison Report Between HSFLT_P13 (SEQ ID NO:20) and NP_(—)002010(SEQ ID NO: 531):

A. An isolated chimeric polypeptide as set forth in HSFLT_P13 (SEQ IDNO:20), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEWWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEITIRDQEAPYLLRNLSDHTVAISSSTTLDCHANGVPEPQITWFKNNIKIQQEPG corresponding to amino acids 1-706 ofNP_(—)002010 (SEQ ID NO: 531), which also corresponds to amino acids1-706 of HSFLT_P13 (SEQ ID NO:20), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQID NO: 466) corresponding to amino acids 707-736 of HSFLT_P13 (SEQ IDNO:20), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P13(SEQ ID NO:20), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence KRLFFLPFIISHLSSAPLSLNSPVTCFQYV (SEQ ID NO:466) of HSFLT_P13 (SEQ ID NO:20).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P13 (SEQ ID NO:20) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 30,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P13 (SEQ ID NO:20) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 30 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P13 (SEQ ID NO:20), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 31 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 31 Glycosylation site(s) Position(s) on known Position(s) on aminoacid sequence Present in variant protein? variant protein 100 Yes 100164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417 Yes 417474 Yes 474 547 Yes 547 597 Yes 597 620 Yes 620 625 Yes 625 666 Yes 666

The phosphorylation sites of variant protein HSFLT_P13 (SEQ ID NO:20),as compared to the known protein, are described in Table 32 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 32 Phosphorylation site(s) Position(s) on known amino acidsequence Present in variant protein? 1053 No 1169 No 1213 No 1242 No1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 33:

TABLE 33 InterPro domain(s) Domain description Analysis type Position(s)on protein Vascular endothelial growth FPrintScan 89-107, 125-136,factor receptor, VEGFR 184-194, 242-254, 390-407, 448-462 Vascularendothelial growth FPrintScan 26-41, 79-93, 130-155, factor receptor 1,VEGFR1 224-247, 273-290, 350-370, 375-389 Immunoglobulin-like HMMPfam245-313, 570-638, 675-734 Immunoglobulin V-type HMMSmart 247-313,572-638 Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412,568-643, 673-725 Immunoglobulin subtype HMMSmart 38-129, 143-224,237-329, 344-425, 439-553, 562-658 Immunoglobulin-like ProfileScan32-107, 230-327, 349-404, 428-553, 556-654, 661-732

Variant protein HSFLT_P13 (SEQ ID NO:20) is encoded by the followingtranscript(s): HSFLT_T17 (SEQ ID NO:7), for which the coding portionstarts at position 315 and ends at position 2522. The transcript alsohas the following SNPs as listed in Table 34 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P13 (SEQ IDNO:20) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 34 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence -> C  823 T -> C 1063, 1342 A -> G 1165, 1325, 1495 C -> T 1533G -> A 2018

Variant protein HSFLT_P14 (SEQ ID NO:21) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T19 (SEQ ID NO:8). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P14 (SEQ ID NO:21) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P14 (SEQ IDNO:21), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKcorresponding to amino acids 1-517 of VGR1_HUMAN (SEQ ID NO: 359), whichalso corresponds to amino acids 1-517 of HSFLT_P14 (SEQ ID NO:21), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceYLDIRTEEQIFSFIQKTQTLKLTVSCKAAF (SEQ ID NO: 468) corresponding to aminoacids 518-547 of HSFLT_P14 (SEQ ID NO:21), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P14(SEQ ID NO:21), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence YLDIRTEEQIFSFIQKTQTLKLTVSCKAAF (SEQ ID NO:468) of HSFLT_P14 (SEQ ID NO:21).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P14 (SEQ ID NO:21) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 35,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P14 (SEQ ID NO:21) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 35 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P14 (SEQ ID NO:21), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 36 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 36 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 100Yes 100 164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417Yes 417 474 Yes 474 547 No 597 No 620 No 625 No 666 No

The phosphorylation sites of variant protein HSFLT_P14 (SEQ ID NO:21),as compared to the known protein, are described in Table 37 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 37 Phosphorylation site(s) Position(s) on known amino acidsequence Present in variant protein? 1053 No 1169 No 1213 No 1242 No1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 38:

TABLE 38 InterPro domain(s) Position(s) Domain description Analysis typeon protein Vascular endothelial growth factor FPrintScan 89-107,125-136, receptor, VEGFR 184-194, 242-254, 390-407, 448-462 Vascularendothelial growth factor FPrintScan 26-41, 79-93, receptor 1, VEGFR1130-155, 224-247, 273-290, 350-370, 375-389 Immunoglobulin-like HMMPfam245-313 Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412Immunoglobulin subtype HMMSmart 38-129, 143-224, 237-329, 344-425Immunoglobulin-like ProfileScan 32-107, 230-327, 349-404, 428-467

Variant protein HSFLT_P14 (SEQ ID NO:21) is encoded by the followingtranscript(s): HSFLT_T19 (SEQ ID NO:8), for which the coding portionstarts at position 315 and ends at position 1955. The transcript alsohas the following SNPs as listed in Table 39 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P14 (SEQ IDNO:21) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 39 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence -> C  823 T -> C 1063, 1342, A -> G 1165, 1325, 1495, 2465 C ->T 1533

Variant protein HSFLT_P15 (SEQ ID NO:22) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T20 (SEQ ID NO:9). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P15 (SEQ ID NO:22) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P15 (SEQ IDNO:22), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIY corresponding to amino acids 1-329 ofVGR1_HUMAN (SEQ ID NO: 359), which also corresponds to amino acids 1-329of HSFLT_P15 (SEQ ID NO:22), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence GKHSSALPTHAMLSNHCRCLCSLNKSVFCWPRVTLS(SEQ ID NO: 469) corresponding to amino acids 330-365 of HSFLT_P15 (SEQID NO:22), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P15(SEQ ID NO:22), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GKHSSALPTHAMLSNHCRCLCSLNKSVFCWPRVTLS (SEQ IDNO: 469) of HSFLT_P15 (SEQ ID NO:22).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P15 (SEQ ID NO:22) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 40,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P15 (SEQ ID NO:22) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 40 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R

The glycosylation sites of variant protein HSFLT_P15 (SEQ ID NO:22), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 41 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 41 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 100Yes 100 164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 No 417 No474 No 547 No 597 No 620 No 625 No 666 No

The phosphorylation sites of variant protein HSFLT_P15 (SEQ ID NO:22),as compared to the known protein, are described in Table 42 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 42 Phosphorylation site(s) Position(s) on known amino acidsequence Present in variant protein? 1053 No 1169 No 1213 No 1242 No1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 43:

TABLE 43 InterPro domain(s) Position(s) Domain description Analysis typeon protein Vascular endothelial growth factor FPrintScan 89-107,125-136, receptor, VEGFR 184-194, 242-254 Vascular endothelial growthfactor FPrintScan 26-41, 79-93, receptor 1, VEGFR1 130-155, 224-247,273-290 Immunoglobulin C2 type HMMSmart 149-214, 243-318 Immunoglobulinsubtype HMMSmart 38-129, 143-224, 237-329 Immunoglobulin-likeProfileScan 32-107, 230-327

Variant protein HSFLT_P15 (SEQ ID NO:22) is encoded by the followingtranscript(s): HSFLT_T20 (SEQ ID NO:9), for which the coding portionstarts at position 315 and ends at position 1409. The transcript alsohas the following SNPs as listed in Table 44 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P15 (SEQ IDNO:22) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 44 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence -> C 823 T -> C 1063 A -> G 1165

Variant protein HSFLT_P16 (SEQ ID NO:23) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T21 (SEQ ID NO:10). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P16 (SEQ ID NO:23) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P16 (SEQ IDNO:23), comprising an amino acid sequence being at least 90% homologoustoMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHMDLAARNILLSENNVVKICDFGLARDIYNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPIcorresponding to amino acids 906-1338 of VGR1_HUMAN (SEQ ID NO: 359),which also corresponds to amino acids 1-433 of HSFLT_P16 (SEQ ID NO:23).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSFLT_P16 (SEQ ID NO:23), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 45 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 45 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 100No 164 No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No625 No 666 No

The phosphorylation sites of variant protein HSFLT_P16 (SEQ ID NO:23),as compared to the known protein, are described in Table 46 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 46 Phosphorylation site(s) Position(s) on known PresentPosition(s) on amino acid sequence invariant protein? variant protein148 Yes 148 264 Yes 264 308 Yes 308 337 Yes 337 422 Yes 422 428 Yes 428

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 47:

TABLE 47 InterPro domain(s) Position(s) Domain description Analysis typeon protein Protein kinase BlastProDom 1-22, 88-254 Protein kinaseHMMPfam 27-249  Tyrosine protein kinase HMMSmart 1-249 Serine HMMSmart1-253 Protein kinase ProfileScan 1-253 Tyrosine protein kinase, activesite ScanRegExp 113-125 

Variant protein HSFLT_P16 (SEQ ID NO:23) is encoded by the followingtranscript(s): HSFLT_T21 (SEQ ID NO:10), for which the coding portionstarts at position 142 and ends at position 1440. The transcript alsohas the following SNPs as listed in Table 48 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P16 (SEQ IDNO:23) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 48 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> A  177 A -> G 498, 2533, 4052 T -> C 630, 1065 T -> 1589 C-> T 1790 G -> T 2711 T -> G 2958, 2963, 4081 A -> C 3799

Variant protein HSFLT_P17 (SEQ ID NO:24) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T22 (SEQ ID NO:11). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P17 (SEQ ID NO:24) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P17 (SEQ IDNO:24), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKK corresponding to amino acids 1-171 of VGR1_HUMAN(SEQ ID NO: 359), which also corresponds to amino acids 1-171 ofHSFLT_P17 (SEQ ID NO:24), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequenceVNLNTAILSILSLQISIMKFYSFYLSGIISLQTPGLLSGLSCN (SEQ ID NO: 470)corresponding to amino acids 172-214 of HSFLT_P17 (SEQ ID NO:24),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P17(SEQ ID NO:24), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence VNLNTAILSILSLQISIMKFYSFYLSGIISLQTPGLLSGLSCN(SEQ ID NO: 470) of HSFLT_P17 (SEQ ID NO:24).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

The glycosylation sites of variant protein HSFLT_P17 (SEQ ID NO:24), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 49 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 49 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 100 Yes 100164 Yes 164 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620No 625 No 666 No

The phosphorylation sites of variant protein HSFLT_P17 (SEQ ID NO:24),as compared to the known protein, are described in Table 50 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 50 Phosphorylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 1053 No1169 No 1213 No 1242 No 1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 51:

TABLE 51 InterPro domain(s) Analysis Domain description type Position(s)on protein Vascular endothelial growth factor FPrintScan 89-107, 125-136receptor, VEGFR Vascular endothelial growth factor FPrintScan 26-41,79-93, 130-155 receptor 1, VEGFR1 Immunoglobulin-like ProfileScan 32-107

Variant protein HSFLT_P17 (SEQ ID NO:24) is encoded by the followingtranscript(s): HSFLT_T22 (SEQ ID NO:11), for which the coding portionstarts at position 315 and ends at position 956. The transcript also hasthe following SNPs as listed in Table 52 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P17 (SEQ IDNO:24) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 52 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence -> C 823

Variant protein HSFLT_P18 (SEQ ID NO:25) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T23 (SEQ ID NO: 12).An alignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P18 (SEQ ID NO:25) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P18 (SEQ IDNO:25), comprising an amino acid sequence being at least 90% homologoustoMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI corresponding to aminoacids 996-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also corresponds toamino acids 1-343 of HSFLT_P18 (SEQ ID NO:25).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSFLT_P18 (SEQ ID NO:25), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 53 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 53 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 100 No 164No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No 625 No666 No

The phosphorylation sites of variant protein HSFLT_P18 (SEQ ID NO:25),as compared to the known protein, are described in Table 54 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 54 Phosphorylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 58 Yes 58174 Yes 174 218 Yes 218 247 Yes 247 332 Yes 332 338 Yes 338

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 55:

TABLE 55 InterPro domain(s) Domain description Analysis type Position(s)on protein Protein kinase BlastProDom 1-164 Tyrosine protein kinaseFPrintScan 17-35, 66-76, 85-107, 130-152 Protein kinase HMMPfam 1-159Tyrosine protein kinase HMMSmart 1-159 Serine HMMSmart 1-163 Proteinkinase ProfileScan 1-163 Tyrosine protein kinase, active ScanRegExp23-35 site

Variant protein HSFLT_P18 (SEQ ID NO:25) is encoded by the followingtranscript(s): HSFLT_T23 (SEQ ID NO:12), for which the coding portionstarts at position 66 and ends at position 1094. The transcript also hasthe following SNPs as listed in Table 56 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P18 (SEQ IDNO:25) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 56 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence A -> G 152, 2187, 3706 T -> C 284, 719 T -> 1243 C -> T 1444 G-> T 2365 T -> G 2612, 2617, 3735 A -> C 3453

Variant protein HSFLT_P19 (SEQ ID NO:26) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T24 (SEQ ID NO:13). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P19 (SEQ ID NO:26) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P19 (SEQ IDNO:26), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQBIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFIS correspondingto amino acids 1-129 of VGR1_HUMAN (SEQ ID NO: 359), which alsocorresponds to amino acids 1-129 of HSFLT_P19 (SEQ ID NO:26), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGKTSIFYILFAFALQMSHKSTLIHWKGCFPSEYERNGLGKRFHPSCRBFRGCQF (SEQ ID NO: 471)corresponding to amino acids 130-183 of HSFLT_P19 (SEQ ID NO:26),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P19(SEQ ID NO:26), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceGKTSIFYILFAFALQMSHKSTLIHWKGCFPSEYERNGLGKRFHPSCRHFRGCQF (SEQ ID NO: 471)of HSFLT_P19 (SEQ ID NO:26).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is membrane.

The glycosylation sites of variant protein HSFLT_P19 (SEQ ID NO:26), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 57 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 57 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 100 Yes 100164 No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No625 No 666 No

The phosphorylation sites of variant protein HSFLT_P19 (SEQ ID NO:26),as compared to the known protein, are described in Table 58 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 58 Phosphorylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 1053 No1169 No 1213 No 1242 No 1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 59:

TABLE 59 InterPro domain(s) Analysis Domain description type Position(s)on protein Vascular endothelial growth factor FPrintScan 89-107, 125-136receptor, VEGFR Vascular endothelial growth factor FPrintScan 26-41,79-93 receptor 1, VEGFR1 Immunoglobulin-like ProfileScan 32-107

Variant protein HSFLT_P19 (SEQ ID NO:26) is encoded by the followingtranscript(s): HSFLT_T24 (SEQ ID NO:13), for which the coding portionstarts at position 315 and ends at position 863.

Variant protein HSFLT_P20 (SEQ ID NO:27) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T25 (SEQ ID NO:14). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P20 (SEQ ID NO:27) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P20 (SEQ IDNO:27), comprising an amino acid sequence being at least 90% homologoustoMLDCWBRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI correspondingto amino acids 1133-1338 of VGR1_HUMAN (SEQ ID NO: 359), which alsocorresponds to amino acids 1-206 of HSFLT_P20 (SEQ ID NO:27).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSFLT_P20 (SEQ ID NO:27), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 60 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 60 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 100 No 164No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No 625 No666 No

The phosphorylation sites of variant protein HSFLT_P20 (SEQ ID NO:27),as compared to the known protein, are described in Table 61 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 61 Phosphorylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 37 Yes 3781 Yes 81 110 Yes 110 195 Yes 195 201 Yes 201 1053 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 62:

TABLE 62 InterPro domain(s) Domain description Analysis type Position(s)on protein Protein kinase BlastProDom 1-27

Variant protein HSFLT_P20 (SEQ ID NO:27) is encoded by the followingtranscript(s): HSFLT_T25 (SEQ ID NO:14), for which coding portion startsat position 693 and ends at position 1310. The transcript also has thefollowing SNPs as listed in Table 63 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HSFLT_P20 (SEQ ID NO:27)sequence provides support for the deduced sequence of this variantprotein according to the present invention).

TABLE 63 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence T -> C  935 T -> 1459 C -> T 1660 A -> G 2403, 3922 G -> T 2581T -> G 2828, 2833, 3951 A -> C 3669

Variant protein HSFLT_P21 (SEQ ID NO:28) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T26 (SEQ ID NO:15). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P21 (SEQ ID NO:28) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P21 (SEQ IDNO:28), comprising an amino acid sequence being at least 90% homologoustoMSLERIKTFEELLPNATSMFDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPI corresponding to aminoacids 1220-1338 of VGR1_HUMAN (SEQ ID NO: 359), which also correspondsto amino acids 1-119 of HSFLT_P21 (SEQ ID NO:28).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSFLT_P21 (SEQ ID NO:28), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 64 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 64 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 100 No 164No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No 625 No666 No

The phosphorylation sites of variant protein HSFLT_P21 (SEQ ID NO:28),as compared to the known protein, are described in Table 65 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 65 Phosphorylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 23 Yes 23108 Yes 108 114 Yes 114 1053 No 1169 No 1213 No

Variant protein HSFLT_P21 (SEQ ID NO:28) is encoded by the followingtranscript(s): HSFLT_T26 (SEQ ID NO:15), for which the coding portionstarts at position 265 and ends at position 621. The transcript also hasthe following SNPs as listed in Table 66 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P21 (SEQ IDNO:28) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 66 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A  36 T -> C 209, 246 T ->  770 C -> T  971 A -> G 1714,3233 G -> T 1892 T -> G 2139, 2144, 3262 A -> C 2980

Variant protein HSFLT_P41 (SEQ ID NO:29) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T21 (SEQ ID NO:10). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P41 (SEQ ID NO:29) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P41 (SEQ IDNO:29), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence LWAACPAQACSGNAGQERGGLQSAAGLPSQPSCFLQTGVGLANQ (SEQ IDNO: 577) corresponding to amino acids 1-44 of HSFLT_P41 (SEQ ID NO:29),and a second amino acid sequence being at least 90% homologous toGPLMVIVEYCKYGNLSNYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLSDVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCMIIDLAARNELLSENNVVKICDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGSPYPGVQMDEDFCSRLREGRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLLQANVQQDGKDYIPINAILTGNSGFTYSTPAFSEDFFKESISAPKFNSGSSDDVRYVNAFKFMSLERIKTFEELLPNATSMPDDYQGDSSTLLASPMLKRFTWTDSKPKASLKIDLRVTSKSKESGLSDVSRPSFCHSSCGHVSEGKRRFTYDHAELERKIACCSPPPDYNSVVLYSTPPIcorresponding to amino acids 903-1338 of VGR1_HUMAN (SEQ ID NO: 359),which also corresponds to amino acids 45-480 of HSFLT_P41 (SEQ IDNO:29), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSFLT_P41 (SEQ IDNO:29), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceLWAACPAQACSGNAGQERGGLQSAAGLPSQPSCFLQTGVGLANQ (SEQ ID NO: 577) ofHSFLT_P41 (SEQ ID NO:29).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSFLT_P41 (SEQ ID NO:29), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 67 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 67 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 100 No 164No 196 No 251 No 323 No 402 No 417 No 474 No 547 No 597 No 620 No 625 No666 No

The phosphorylation sites of variant protein HSFLT_P41 (SEQ ID NO:29),as compared to the known protein, are described in Table 68 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 68 Phosphorylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 195 Yes 195311 Yes 311 355 Yes 355 384 Yes 384 469 Yes 469 475 Yes 475

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 69:

TABLE 69 InterPro domain(s) Domain description Analysis type Position(s)on protein Protein kinase BlastProDom 45-69, 135-301 Protein kinaseHMMPfam  74-296 Tyrosine protein kinase HMMSmart  9-296 Serine HMMSmart 48-300 Protein kinase ProfileScan  1-300 Tyrosine protein kinase,ScanRegExp 160-172 active site

Variant protein HSFLT_P41 (SEQ ID NO:29) is encoded by the followingtranscript(s): HSFLT_T21 (SEQ ID NO:10), coding portion starts atposition 1 and ends at position 1440. The transcript also has thefollowing SNPs as listed in Table 70 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HSFLT_P41 (SEQ ID NO:29)sequence provides support for the deduced sequence of this variantprotein according to the present invention).

TABLE 70 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> A  177 A -> G 498, 2533, 4052 T -> C 630, 1065 T -> 1589 C-> T 1790 G -> T 2711 T -> G 2958, 2963, 4081 A -> C 3799

Variant protein HSFLT_P48 (SEQ ID NO:30) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T7 (SEQ ID NO: 1). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P48 (SEQ ID NO:30) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P48 (SEQ IDNO:30), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKcorresponding to amino acids 1-517 of VGR1_HUMAN (SEQ ID NO: 359), whichalso corresponds to amino acids 1-517 of HSFLT_P48 (SEQ ID NO:30), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceLPPANSSFMLPPTSFSSNYFHFLP (SEQ ID NO: 472) corresponding to amino acids518-541 of HSFLT_P48 (SEQ ID NO:30), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P48(SEQ ID NO:30), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence LPPANSSFMLPPTSFSSNYFHFLP (SEQ ID NO: 472) ofHSFLT_P48 (SEQ ID NO:30).

The comparison between HSFLT_P48 (SEQ ID NO:30) and Q16333_HUMAN (SEQ IDNO: 552), given below, shows that the two sequences have no homology.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P48 (SEQ ID NO:30) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 71,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P48 (SEQ ID NO:30) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 71 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P48 (SEQ ID NO:30), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 72 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 72 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 100 Yes 100164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417 Yes 417474 Yes 474 547 No 597 No 620 No 625 No 666 No

The phosphorylation sites of variant protein HSFLT_P48 (SEQ ID NO:30),as compared to the known protein, are described in Table 73 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 73 Phosphorylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 1053 No 1169No 1213 No 1242 No 1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 74:

TABLE 74 InterPro domain(s) Analysis Domain description type Position(s)on protein Vascular endothelial FPrintScan 89-107, 125-136, 184-194,growth factor 242-254, 390-407, 448-462 receptor, VEGFR Vascularendothelial FPrintScan 26-41, 79-93, 130-155, 224-247, growth factor273-290, 350-370, 375-389 receptor 1, VEGFR1 Immunoglobulin-like HMMPfam245-313 Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412Immunoglobulin subtype HMMSmart 38-129, 143-224, 237-329, 344-425Immunoglobulin-like ProfileScan 32-107, 230-327, 349-404, 428-467

Variant protein HSFLT_P48 (SEQ ID NO:30) is encoded by the followingtranscript(s): HSFLT_T7 (SEQ ID NO:1), for which the coding portionstarts at position 315 and ends at position 1937. The transcript alsohas the following SNPs as listed in Table 75 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P48 (SEQ IDNO:30) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 75 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence -> C  823 T -> C 1063, 1342, 2939, 3603, 4038 A -> G 1165,1325, 1495, 2677, 3471, 5506, 7025 C -> T 1533, 4763 G -> A 2103 C -> A3150 T -> 4562 G -> T 5684 T -> G 5931, 5936, 7054 A -> C 6772

Variant protein HSFLT_P49 (SEQ ID NO:31) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSFLT_T8 (SEQ ID NO:2). Analignment is given to the known protein (Vascular endothelial growthfactor receptor 1 precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSFLT_P49 (SEQ ID NO:31) and VGR1_HUMAN(SEQ ID NO: 359):

A. An isolated chimeric polypeptide as set forth in HSFLT_P49 (SEQ IDNO:31), comprising a first amino acid sequence being at least 90%homologous toMVSYWDTGVLLCALLSCLLLTGSSSGSKLKDPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSITKSACGRNGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKKKETESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSNSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWBPCNHNHSEARCDFCSNNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYIT corresponding to amino acids 1-553 ofVGR1_HUMAN (SEQ ID NO: 359), which also corresponds to amino acids 1-553of HSFLT_P49 (SEQ ID NO:31), and a second amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence ELSNFECLHPCSQE (SEQ ID NO: 473)corresponding to amino acids 554-567 of HSFLT_P49 (SEQ ID NO:31),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSFLT_P49(SEQ ID NO:31), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence ELSNFECLHPCSQE (SEQ ID NO: 473) of HSFLT_P49(SEQ ID NO:31).

HSFLT_P49 (SEQ ID NO:31) and Q16332_HUMAN (SEQ ID NO: 553) do not showhomology.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSFLT_P49 (SEQ ID NO:31) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 76,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSFLT_P49 (SEQ ID NO:31) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 76 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 250 L -> P 284 Q -> R 343 V -> A 394 D -> G

The glycosylation sites of variant protein HSFLT_P49 (SEQ ID NO:31), ascompared to the known protein Vascular endothelial growth factorreceptor 1 precursor, are described in Table 77 (given according totheir position(s) on the amino acid sequence in the first column; thesecond column indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 77 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 100 Yes 100164 Yes 164 196 Yes 196 251 Yes 251 323 Yes 323 402 Yes 402 417 Yes 417474 Yes 474 547 Yes 547 597 No 620 No 625 No 666 No

The phosphorylation sites of variant protein HSFLT_P49 (SEQ ID NO:31),as compared to the known protein, are described in Table 78 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 78 Phosphorylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 1053No 1169 No 1213 No 1242 No 1327 No 1333 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 79:

TABLE 79 InterPro domain(s) Domain description Analysis type Position(s)on protein Vascular endothelial FPrintScan 89-107, 125-136, 184-194,growth factor 242-254, 390-407, receptor, VEGFR 448-462 Vascularendothelial FPrintScan 26-41, 79-93, 130-155, growth factor 224-247,273-290, receptor 1, VEGFR1 350-370, 375-389 Immunoglobulin-like HMMPfam245-313 Immunoglobulin C2 type HMMSmart 149-214, 243-318, 348-412Immunoglobulin subtype HMMSmart 38-129, 143-224, 237-329, 344-425,439-553 Immunoglobulin-like ProfileScan 32-107, 230-327, 349-404,428-553

Variant protein HSFLT_P49 (SEQ ID NO:31) is encoded by the followingtranscript(s): HSFLT_T8 (SEQ ID NO:2), for which the coding portionstarts at position 315 and ends at position 2015. The transcript alsohas the following SNPs as listed in Table 80 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSFLT_P49 (SEQ IDNO:31) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 80 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence -> C  823 T -> C 1063, 1342, 2919, 3583, 4018 A -> G 1165,1325, 1495, 2657, 3451, 5486, 7005 C -> T 1533, 4743 G -> A 2083 C -> A3130 T -> 4542 G -> T 5664 T -> G 5911, 5916, 7034 A -> C 6752

As noted above, cluster HSFLT features 58 segment(s), which were listedin Table 7 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segment 20 according to the present invention is now provided.

Segment cluster HSFLT_N20 (SEQ ID NO:42) according to the presentinvention is supported by 2 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSFLT_T20 (SEQ ID NO:9). Table 81 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 81 Segment location on transcripts Segment Segment starting endingTranscript name position position HSFLT_T20 (SEQ ID NO: 9) 1303 1731

FIG. 4 shows the structure of the various HSFLT variants describedabove, for both mRNA and protein. “WT” refers to the known protein/mRNA.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

Expression of Homo sapiens fms-Related Tyrosine Kinase 1 (VascularEndothelial Growth Factor/Vascular Permeability Factor Receptor) (FLT1)HSFLT Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSFLT_seg20 (SEQ ID NO:363) in Different Normal Tissues

Expression of Homo sapiens fins-related tyrosine kinase 1 (vascularendothelial growth factor/vascular permeability factor receptor) (FLT1)transcripts detectable by or according to seg20—HSFLT_seg20 (SEQ IDNO:363) amplicon and primers HSFLT_seg20F (SEQ ID NO:361) andHSFLT_seg20R (SEQ ID NO:362) was measured by real time PCR. In parallelthe expression of four housekeeping genes—SDHA (GenBank Accession No.NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)),Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (SEQ ID NO:368)(GenBank Accession No. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ IDNO:368) amplicon) and TATA (SEQ ID NO:370) box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the placenta samples (samplenumbers 30, 31 and 32, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the placenta samples.FIG. 5 shows expression of Homo sapiens fms-related tyrosine kinase 1(vascular endothelial growth factor/vascular permeability factorreceptor) (FLT1) transcripts detectable by or according toseg20—HSFLT_seg20 (SEQ ID NO:363) amplicon and primers HSFLT_seg20F (SEQID NO:361) and HSFLT_seg20R (SEQ ID NO:362) on a normal panel.

Forward Primer (HSFLT_seg20F (SEQ ID NO:361)): GCATAGTTCAGCGTTGCCAACReverse Primer (HSFLT_seg20R (SEQ ID NO:362)): CCATGGCCAAGCTGTATTCAAmplicon (HSFLT_seg20 (SEQ ID NO:363)):GCATAGTTCAGCGTTGCCAACTCATGCTATGCTTTCTAATCATTGTAGATGTCTGTGTTCTCTAAATAAGTCAGTTTTCTGTTGGCCAAGAGTTACATTATCATGAATGAATACAGCTTGGCCATGG

Homo sapiens fms-related tyrosine kinase 1 (vascular endothelial growthfactor/vascular permeability factor receptor) (FLT1) transcriptsdetectable by or according to seg20—HSFLT_seg20 (SEQ ID NO:363) ampliconand primers HSFLT_seg20F (SEQ ID NO:361) and HSFLT_seg20R (SEQ IDNO:362) did not show any differential expression in one experimentcarried out with each of the following cancer panels: lung cancer,breast cancer, colon cancer and ovary cancer.

Description for Cluster HSI1RA

Cluster HSI1RA features 4 transcript(s) and 25 segment(s) of interest,the names for which are given in Tables 82 and 83, respectively. Theselected protein variants are given in table 84.

TABLE 82 Transcripts of interest Transcript Name HSI1RA_T2 (SEQ ID NO:61) HSI1RA_T13 (SEQ ID NO: 62) HSI1RA_T16 (SEQ ID NO: 63) HSI1RA_T19(SEQ ID NO: 64)

TABLE 83 Segments of interest Segment Name HSI1RA_N13 (SEQ ID NO: 71)HSI1RA_N17 (SEQ ID NO: 73) HSI1RA_N19 (SEQ ID NO: 74) HSI1RA_N20 (SEQ IDNO: 75) HSI1RA_N24 (SEQ ID NO: 78) HSI1RA_N28 (SEQ ID NO: 82) HSI1RA_N38(SEQ ID NO: 89) HSI1RA_N39 (SEQ ID NO: 90) HSI1RA_N40 (SEQ ID NO: 91)HSI1RA_N41 (SEQ ID NO: 92) HSI1RA_N44 (SEQ ID NO: 95) HSI1RA_N15 (SEQ IDNO: 72) HSI1RA_N21 (SEQ ID NO: 76) HSI1RA_N23 (SEQ ID NO: 77) HSI1RA_N25(SEQ ID NO: 79) HSI1RA_N26 (SEQ ID NO: 80) HSI1RA_N27 (SEQ ID NO: 81)HSI1RA_N29 (SEQ ID NO: 83) HSI1RA_N30 (SEQ ID NO: 84) HSI1RA_N31 (SEQ IDNO: 85) HSI1RA_N35 (SEQ ID NO: 86) HSI1RA_N36 (SEQ ID NO: 87) HSI1RA_N37(SEQ ID NO: 88) HSI1RA_N42 (SEQ ID NO: 93) HSI1RA_N43 (SEQ ID NO: 94)

TABLE 84 Proteins of interest Protein Name Corresponding Transcript(s)HSI1RA_P5 (SEQ ID NO: 65) HSI1RA_T13 (SEQ ID NO: 62); HSI1RA_T16 (SEQ IDNO: 63) HSI1RA_P6 (SEQ ID NO: 66) HSI1RA_T16 (SEQ ID NO: 63) HSI1RA_P13(SEQ ID NO: 67) HSI1RA_T13 (SEQ ID NO: 62) HSI1RA_P14 (SEQ ID NO: 68)HSI1RA_T2 (SEQ ID NO: 61) HSI1RA_P16 (SEQ ID NO: 69) HSI1RA_T19 (SEQ IDNO: 64) HSI1RA_P17 (SEQ ID NO: 70) HSI1RA_T19 (SEQ ID NO: 64)

These sequences are variants of the known protein Interleukin-1 receptorantagonist protein precursor (SwissProt accession identifier IL1X_HUMAN(SEQ ID NO: 372); known also according to the synonyms IL-1ra; IRAP; IL1inhibitor; IL-1RN; ICIL-1RA), referred to herein as the previously knownprotein.

Protein Interleukin-1 receptor antagonist protein precursor inhibits theactivity of IL-1 by binding to its receptor. Protein Interleukin-1receptor antagonist protein precursor localization is believed to beSecreted for isoform 1; and Cytoplasmic forisoforms 2, 3 and 4.

The known Interleukin-1 receptor antagonist protein also has thefollowing indication(s) and/or potential therapeutic use(s): Arthritis,osteo; Arthritis, rheumatoid; Asthma; Inflammation, general;Inflammatory bowel disease; Transplant rejection, bone marrow;Unspecified. It has been investigated for clinical/therapeutic use inhumans, for example as a target for an antibody or small molecule,and/or as a direct therapeutic; available information related to theseinvestigations is as follows. Potential pharmaceutically related ortherapeutically related activity or activities of the previously knownprotein are as follows: Interleukin 1 receptor antagonist. A therapeuticrole for a protein represented by the cluster has been predicted. Thecluster was assigned this field because there was information in thedrug database or the public databases (e.g., described herein above)that this protein, or part thereof, is used or can be used for apotential therapeutic indication: Anti-inflammatory; Antiallergic,non-asthma; Antiarthritic, immunological; Antiasthma; Cytokine;Formulation, conjugate, pegylated; GI inflammatory/bowel disorders;Immunosuppressant; Recombinant interleukin.

According to optional embodiments of the present invention, variants ofthis cluster according to the present invention (amino acid and/ornucleic acid sequences of HSI1RA) may optionally have one or more of thefollowing utilities, as described with regard to the Table 85 below. Itshould be noted that these utilities are optionally and preferablysuitable for human and non-human animals as subjects, except whereotherwise noted. The reasoning is described with regard to biologicaland/or physiological and/or other information about the known protein,but is given to demonstrate particular diagnostic utility for thevariants according to the present invention.

TABLE 85 of Utilities for Variants of HSI1RA, related to Interleukin-1receptor antagonist protein precursor Dx field Explanation RefPrediction of response to Genetic polymorphisms, which Ann Rheum Dis.2003 enteracept in rheumatoid arthritis may influence the balance ofJun; 62(6): 526-9. patients: IL1RA expression, are associatedTheranostics non-responsiveness (p < 0.05) to etanercept (TNF blockingagent) treatment A surrogate marker for treatment Treatment with acombination of Cells Tissues Organs. with a combination of infliximabinfliximab and methotrexate 2005; 180(1): 22-30 and methotrexate.reduces TMJ (temporomandibular joint) pain in RA in association with anincrease in IL-1ra in synovial fluid and plasma. Over expressed in lungcancer Significance: 7E−8 Proc Natl Acad Sci USA. 2001 metastasis Nov20; 98(24): 13790-5.

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HSI1RA) may optionally have one or moreof the following utilities: this marker could be used as a surrogatemarker for determining the efficacy of treatment for acute and chronicinterleukin-1 (IL-1)-mediated inflammatory diseases, including but notlimited to the following: autoimmune diseases; acute pancreatitis; ALS(Amyotrophic Lateral Sclerosis, also known as Lou Gehrig's Disease);Alzheimer's disease; cachexia/anorexia; asthma; atherosclerosis; chronicfatigue syndrome, fever; diabetes (e.g., insulin-dependent diabetes);glomerulonephritis; graft versus host rejection; hemorrhagic shock;hyperalgesia, inflammatory bowel disease; inflammatory conditions of ajoint including osteoarthritis, psoriatic arthritis and rheumatoidarthritis; ischemic injury, including cerebral ischemia (e.g., braininjury as a result of trauma, epilepsy, hemorrhage or stroke, each ofwhich may lead to neurodegeneration); lung diseases (e.g., ARDS (adultrespiratory distress syndrome)); multiple myeloma; multiple sclerosis;myelogenous leukemia (e.g., AML (Acute Myelogenous Leukemia) and CML(Chronic Myelogenous Leukemia)) and other leukemias; myopathies (e.g.,muscle protein metabolism, especially in sepsis); osteoporosis;Parkinson's disease; chronic pain; pre-term labor; psoriasis;reperfusion injury; septic shock; side effects from radiation therapy,temporal mandibular joint disease, tumor metastasis; or an inflammatorycondition resulting from strain, sprain, cartilage damage, trauma,orthopedic surgery, infection or other disease processes.

It is suitable as a surrogate marker because it has been shown to beable to block the IL1 receptor in PCT Application No. WO 05/019259 andhence its presence is clearly related to the mechanism of action of IL1and its receptor in the body.

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HSI1RA) may optionally be used as atheranostic, measured in subjects prior treatment in order to predictthe response to the treatment. It may be measured in various subjectsundergoing different IL1-related treatments, such as hydroxychloroquine(plaquenil), sulfasalazine, methotrexate, leflunomide (Arava), lesscommonly used DMARDS include azathioprine, D-penicillamine, gold salts,minocycline and cyclosporine, NSAIDS (COX-2 Inhibitors), biologic agents(etanercept (Enbrel), infliximab (Remicade) and Anakinra), or notreatment, to determine whether there is a correlation between theefficacy of various treatments and the level of IL1-Ra splice variantsin the body.

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HSI1RA) may optionally have one or moreof the following utilities, some of which are related to utilitiesdescribed above. It should be noted that these utilities are optionallyand preferably suitable for human and non-human animals as subjects,except where otherwise noted.

There is a large body of evidence currently available which supports therole of IL-1 as a major mediator of the systemic response to diseasessuch as sepsis and pancreatitis and as an activator of the remainingmembers of the cytokine cascade (Dinarello C A 1994 FASEB J8:1314-1325).

Because IL-1 is involved in the body's response to inflammation, it isnot surprising that excessive production or activity of IL-1 can lead toinflammatory diseases. A non-exclusive list of acute and chronicinterleukin-1 (IL-1)-mediated inflammatory diseases includes but is notlimited to the following: autoimmune diseases; acute pancreatitis; ALS(Amyotrophic Lateral Sclerosis, also known as Lou Gehrig's Disease);Alzheimer's disease; cachexia/anorexia; asthma; atherosclerosis; chronicfatigue syndrome, fever; diabetes (e.g., insulin-dependent diabetes);glomerulonephritis; graft versus host rejection; hemorrhagic shock;hyperalgesia, inflammatory bowel disease; inflammatory conditions of ajoint including osteoarthritis, psoriatic arthritis and rheumatoidarthritis; ischemic injury, including cerebral ischemia (e.g., braininjury as a result of trauma, epilepsy, hemorrhage or stroke, each ofwhich may lead to neurodegeneration); lung diseases (e.g., ARDS (adultrespiratory distress syndrome)); multiple myeloma; multiple sclerosis;myelogenous leukemia (e.g., AML (Acute Myelogenous Leukemia) and CML(Chronic Myelogenous Leukemia)) and other leukemias; myopathies (e.g.,muscle protein metabolism, especially in sepsis); osteoporosis;Parkinson's disease; chronic pain; pre-term labor; psoriasis;reperfusion injury; septic shock; side effects from radiation therapy,temporal mandibular joint disease, tumor metastasis; or an inflammatorycondition resulting from strain, sprain, cartilage damage, trauma,orthopedic surgery, infection or other disease processes.

In normal homeostasis, the actions of IL-1 are maintained in balance byIL-1ra, other natural IL-1 inhibitors (IL-1RII, circulating solubleIL-1RI and IL-1RII) and a network of anti-inflammatory cytokines.However, in rheumatoid arthritis, an imbalance exists in which IL-1 ispresent in the synovial fluid at a rate 9 times higher than IL-1ra. Thisimbalance favors agonist-derived inflammation and destruction.Therefore, clinical implications for an imbalance between IL-1 andIL-1Ra include but are not limited to, rheumatoid arthritis, asthma,inflammatory bowel disease, transplant rejection, and bone marrowtransplantation. It is also believed that this imbalance may beimplicated in cancers such as leukemias and myelomas, and possibly alsoin arteriosclerosis, Alzheimer's disease and septic shock.

U.S. Pat. No. 6,599,873, hereby incorporated by reference as if fullyset forth herein, describes a number of pathological conditionsassociated with IL-1 production. For example, again without wishing tobe limited by a single hypothesis, IL-1 may increase the level ofcollagenase in an arthritic joint, as well as being potentially involvedin immunopathology of rheumatoid arthritis. IL-1 may alter endothelialcell function and thereby cause the migration of leukocytes andlymphocytes into the synovial tissue, as well as causing macrophages toaccumulate in the synovial lining. In addition, IL-1 may cause capillarygrowth and vascularization. IL-1 may also be at least partiallyresponsible for tissue damage in rheumatoid arthritis, by stimulatingrelease of enzymes from fibroblasts and chondrocytes.

IL-1 may also be associated with damage and/or pathological functioningin various types of arthritis. Excessive IL-1 production has beendemonstrated in the skin of patients with psoriasis and high levels ofIL-1 can be found in the synovial fluid of patients with psoriaticarthritis. IL-1 released by cells in the inflamed synovium in psoriaticarthritis may mediate tissue destruction through stimulation of enzymerelease from other cells. The joint pathology of Reiter's syndrome issimilar to that seen in psoriatic arthritis and in rheumatoid arthritis.IL-1 has been implicated as a mediator of tissue destruction in thesethree different forms of inflammatory arthritis. Moreover, IL-1 may befound in the synovial fluid of patients with osteoarthritis. The releaseof IL-1 by chondrocytes has been implicated in the destruction ofarticular cartilage in this disease.

IL-1 may also increase the severity of autoimmune diseases. For example,decreased IL-1 production has been described from peripheral blood cellsin persons suffering from systemic lupus erythematosus. Moreover, someof the alterations in B lymphocyte function may be related toabnormalities in IL-1 production or IL-1 availability.

Excessive IL-1 production has been demonstrated in the peripheralmonocytes of patients with scleroderma, and IL-1 has been implicated asa possible agent of fibrosis through stimulation of collagen productionby fibroblasts. The mechanism of tissue damage in dermatomyositis mightalso involve cell-mediated immunity and IL-1 may therefore be involvedas a mediator in this pathophysiological process.

Acute and chronic interstitial lung disease is characterized byexcessive collagen production by lung fibroblasts which may bestimulated by IL-1. Recent studies on an animal model of pulmonaryhypertension indicate that IL-1 may be responsible for induction ofendothelial cell changes that result in narrowing of pulmonary arteries.It is this narrowing that leads to pulmonary hypertension and furthersecondary damage. Thus, IL-1 inhibitors could be useful in treatingthese lung diseases.

Recent studies have described that IL-1 is capable of directly damagingthe beta cells in the Islets of Langerhans that are responsible for theproduction of insulin. IL-1 damage to the cells is now hypothesized tobe a primary event in the acute phase of juvenile diabetes mellitus.

Monocyte and macrophage infiltration in the kidneys predominates in manyforms of acute and chronic glomerulonephritis. IL-1 release by thesecells may result in local accumulation of other inflammatory cells,eventually leading to inflammatory damage and fibrotic reaction in thekidneys.

It has been demonstrated that the crystals found in tissues or fluids ingout or pseudogout can directly stimulate macrophages to release IL-1.Thus, IL-1 may be an important mediator in the inflammatory cycle inthese diseases.

IL-1 is one of the important endocenous pyrogens and may be responsiblefor inducing the marked decree of fever seen in some infectious diseasessuch as acute febrile illnesses due to bacteria or viruses.

Sarcoidosis is characterized by granulomatous lesions in many differentorgans in the body. IL-1 has been shown to be capable of inducinggranuloma formation in vitro and may be involved in this process inpatients with sarcoidosis.

Excessive IL-1 production has been demonstrated in peripheral monocytesfrom both Crohn's disease and ulcerative colitis. Local IL-1 release inthe intestine may be an important mediator in stimulating theinflammatory cycle in these diseases.

Certain lymphomas are characterized by fever, osteoporosis and evensecondary arthritis. Excessive IL-1 release has been demonstrated bysome lymphoma cells in vitro and may be responsible for some of theclinical manifestations of these malignancies. Also, IL-1 production bysome malignant lymphocytes may be responsible for some of the fever,acute phase response and cachexia seen with leukemias.

IL-1 release by astrocytes in the brain is thought to be responsible forinducing the fibrosis that may result after damage to the brain fromvascular occlusion.

These findings have also been supported in animal models. For example,IL-1ra deficient mice spontaneously develop autoimmune diseases similarto R.A (rheumatoid arthritis) and arthritis. Immune colitis in rabbitsdepends on production of IL-1 and is ameliorated by exogenousadministration of IL-1Ra.

Unfortunately, IL-1Ra itself has a number of drawbacks as a therapeuticmolecule. For example, a large excess of IL-1Ra is required to block theeffect of IL-1. The antagonist has a short (6 hours) half-life in bloodplasma. Also, daily injections are required to sustain a therapeuticeffect.

Since as described herein above, interleukin-1 is involved in manypathological conditions, and since IL-1Ra itself is deficient as atherapeutic protein, various modes of inactivation of IL-1, togetherwith advanced methods of applications thereof are therefore required forthe treatment of different IL-1 mediated diseases.

U.S. Pat. Nos. 5,747,444 and 5,817,306 describe a method for treatinggraft versus host disease by administering a recombinant IL-Ra; althoughsuch treatment may be effective from the point of view of the biologicalmechanism, as noted above such treatment has many practical barriers toactual clinical efficacy.

U.S. Pat. No. 5,872,095 discloses a method for reducing reperfusioninjury, as well as methods for inhibiting IL-1 induced expression of aleukocyte adhesion molecule by endothelial cells, treating diseasestates resulting from IL-1 induced adhesion of leukocytes to endothelialcells, and treating arthritis, all by administering a specific type ofIL-1 Ra variant.

U.S. Pat. No. 6,159,460 describes the use of the wild type IL-1 receptorantagonist for treatment of reperfusion injury. Thus, different types ofIL-1 Ra variants may be expected to be useful for the treatment ofreperfusion injury.

U.S. Pat. No. 6,027,712 describes localized treatment of inflamedmucosal tissue lining a cavity with the ear, nose or sinus with IL-1Rausing a special formulation of aerosol.

U.S. Pat. No. 5,747,072 describes a method of reducing an inflammatoryresponse in a joint by administering to the joint a recombinantadenoviral vector comprising an expression control sequence operativelylinked to a gene that encodes an IL-1 receptor antagonist, andexpressing said IL-1Ra at a level sufficient to reduce an inflammatoryresponse in said joint. U.S. Pat. No. 6,096,728 provides pharmaceuticalcompositions comprising synergistic amounts of a hyaluronan or a saltthereof, and an IL-1Ra.

The level of IL-1 receptor antagonist within a cell or a tissue may alsohave diagnostic value, for example by diagnosing endometrial cancer bymeasuring the amount of intracellular IL-1Ra present in endometrialcells from a patient suspected of having said cancer, and comparing theamount to that present in normal endothelial cells is disclosed in U.S.Pat. No. 5,840,496. Methods for diagnosing diseases resulting fromundesirable cell adhesion of IL-1 receptor positive cells to biologicalmaterial, particular to endothelial cells, or autoimmune relateddiseases, or IL-1 dependent cancer by measuring the amount ofintracellular IL-1Ra present are disclosed in U.S. Pat. No. 5,814,469.

According to other optional embodiments of the present invention,variants of HSI1RA cluster according to the present invention (aminoacid and/or nucleic acid sequences of HSI1RA) may optionally have one ormore of the diagnostic utilities, for example by diagnosing IL-1 relateddisease or disorder.

According to yet another embodiment, the IL-1 related disease ordisorder is selected from the group consisting of acute pancreatitis;ALS; Alzheimer's disease; cachexia/anorexia; asthma; atherosclerosis;chronic fatigue syndrome; diabetes (e.g., insulin diabetes);glomerulonephritis; graft versus host rejection; hemorrhagic shock;hyperalgesia, inflammatory bowel disease; inflammatory conditions of ajoint including osteoarthritis, psoriatic arthritis and rheumatoidarthritis; ischemic injury, including cerebral ischemia (e.g., braininjury as a result of trauma, epilepsy, hemorrhage or stroke, each ofwhich may lead to neurodegeneration); lung diseases (e.g., ARDS);multiple myeloma; multiple sclerosis; myelogenous (e.g., AML and CML)and other leukemias; myopathies (e.g., muscle protein metabolism,specifically in sepsis); osteoporosis; Parkinson's disease; chronicpain; pre-term labor; psoriasis; reperfusion injury; septic shock; sideeffects from radiation therapy, temporal mandibular joint disease, tumormetastasis; or an inflammatory condition resulting from strain, sprain,cartilage damage, trauma, orthopedic surgery, or infection.

A non-limiting example of such a utility of variants of HSI1RA clusteraccording to the present invention (amino acid and/or nucleic acidsequences of HSI1RA) is detection of brain injury and myocardialinfraction, as described for example in US patent application number20030109420 (hereby incorporated by reference as if fully set forthherein) with regard to the known protein, IL1-Ra. The non-acute stageoptionally and preferably includes (but is not limited to) asymptomaticcoronary artery disease or stable angina, while the acute stageoptionally and preferably includes (but is not limited to) unstableangina and acute myocardial infarction.

Another non-limiting example of such a utility of variants of HSI1RAcluster according to the present invention (amino acid and/or nucleicacid sequences of HSI1RA) is diagnosis and evaluation of stroke andtransient ischemic attacks, as described for example in US patentapplication number 20040219509 (hereby incorporated by reference as iffully set forth herein) with regard to the known protein, IL1-Ra.

Other non-limiting exemplary utilities for HSI1RA variants according tothe present invention are described in greater detail below and alsowith regard to the previous section on clinical utility.

As noted above, cluster HSI1RA features 4 transcript(s), which werelisted in Table 82 above. These transcript(s) encode for protein(s)which are variant(s) of protein Interleukin-1 receptor antagonistprotein precursor. A description of each variant protein according tothe present invention is now provided.

Variant protein HSI1RA_P5 (SEQ ID NO:65) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T13 (SEQ ID NO:62)and HSI1RA_T16 (SEQ ID NO:63). An alignment is given to the knownprotein (Interleukin-1 receptor antagonist protein precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HSI1RA_P5 (SEQ ID NO:65) and IL1X_HUMAN(SEQ ID NO: 372):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P5 (SEQ IDNO:65), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 35-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds toamino acids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 35-64 of HSI1RA_P5 (SEQ ID NO:65), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P5(SEQ ID NO:65), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO:474) of HSI1RA_P5 (SEQ ID NO:65).

2. Comparison Report Between HSI1RA_P5 (SEQ ID NO:65) and NP_(—)776215(SEQ ID NO: 535):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P5 (SEQ IDNO:65), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 1-34 of NP_(—)776215 (SEQ ID NO: 535), which also corresponds toamino acids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 35-64 of HSI1RA_P5 (SEQ ID NO:65), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P5(SEQ ID NO:65), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO:474) of HSI1RA_P5 (SEQ ID NO:65).

3. Comparison Report Between HSI1RA_P5 (SEQ ID NO:65) and NP_(—)000568(SEQ ID NO: 532):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P5 (SEQ IDNO:65), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 17-50 of NP_(—)000568 (SEQ ID NO: 532), which also corresponds toamino acids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 35-64 of HSI1RA_P5 (SEQ ID NO:65), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

4. Comparison Report Between HSI1RA_P5 (SEQ ID NO:65) and NP_(—)776213(SEQ ID NO: 533):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P5 (SEQ IDNO:65), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 38-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds toamino acids 1-34 of HSI1RA_P5 (SEQ ID NO:65), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 35-64 of HSI1RA_P5 (SEQ ID NO:65), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

Variant protein HSI1RA_P5 (SEQ ID NO:65) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 86,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSI1RA_P5 (SEQ ID NO:65) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 86 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 20 Q -> * 42 P -> S 43 M -> T 45 V -> L

The glycosylation sites of variant protein HSI1RA_P5 (SEQ ID NO:65), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 87 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 87 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 88:

TABLE 88 InterPro domain(s) Domain description Analysis type Position(s)on protein Interleukin-1 BlastProDom 1-34

Variant protein HSI1RA_P5 (SEQ ID NO:65) is encoded by the followingtranscript(s): HSI1RA_T13 (SEQ ID NO:62) and HSI1RA_T16 (SEQ ID NO:63),for which the coding portion starts at position 203 and ends at position394. The transcript also has the following SNPs as listed in Table 89(given according to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein HSI1RA_P5 (SEQ ID NO:65) sequence provides support for thededuced sequence of this variant protein according to the presentinvention).

TABLE 89 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 68, 169, 337, 440, 463, 1529, 2014, 2325, 2978 A -> G124, 736, 867, 1621 G -> C 143, 335, 358, 1534 C -> T 260, 326, 481,547, 1643, 1783, 756, 1939, 1945, 2081, 2176 T -> C 271, 330, 437, 1870,1913, 2324 T -> G 399, 2533, 2641 A -> C 402, 574, 1199, 1988, 2398 C ->A 413, 784 G -> T 522 C -> G 868, 2069, 2089, 2152 C -> A 868, 1198 -> T1787 C -> 1846, 2069 T -> 2504, 2705, 2635

The coding portion of transcript HSI1RA_T16 (SEQ ID NO:63) starts atposition 478 and ends at position 669. The transcript also has thefollowing SNPs as listed in Table 90 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HSI1RA_P5 (SEQ ID NO:65)sequence provides support for the deduced sequence of this variantprotein according to the present invention).

TABLE 90 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> G 40, 1143, 2344, 2364, 2427 C -> T 268, 535, 601, 756,822, 1031, 1918, 2058, 2214, 2220, 2356, 2451 G -> A 304, 444, 612, 715,738, 1804, 2289, 2600, 3253 T -> C 546, 605, 712, 2145, 2599, 2188 G ->C 610, 633, 1809 T -> G 674, 2808, 2916 A -> C 677, 849, 1474, 2263,2673 C -> A 688, 1059, 1143, 1473 G -> T 797 A -> G 1011, 1142, 1896 ->T 2062 C -> 2121, 2344 T -> 2779, 2910, 2980

Variant protein HSI1RA_P6 (SEQ ID NO:66) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T16 (SEQ ID NO:63).An alignment is given to the known protein (Interleukin-1 receptorantagonist protein precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSI1RA_P6 (SEQ ID NO:66) and IL1X_HUMAN(SEQ ID NO: 372):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P6 (SEQ IDNO:66), comprising a first amino acid sequence being at least 90%homologous toMEICRGLRSHLITLLLFLFHSETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 1-68 of IL1X_HUMAN (SEQ ID NO: 372), whichalso corresponds to amino acids 1-68 of HSI1RA_P6 (SEQ ID NO:66), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 69-98 of HSI1RA_P6 (SEQ ID NO:66), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P6(SEQ ID NO:66), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO:474) of HSI1RA_P6 (SEQ ID NO:66).

2. Comparison Report Between HSI1RA_P6 (SEQ ID NO:66) and P18510-2 (SEQID NO:373):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P6 (SEQ IDNO:66), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) correspondingto amino acids 1-21 of HSI1RA_P6 (SEQ ID NO:66), a second amino acidsequence being at least 90% homologous toETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 4-50 of P18510-2 (SEQ ID NO:373), which also corresponds to aminoacids 22-68 of HSI1RA_P6 (SEQ ID NO:66), and a third amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQID NO: 474) corresponding to amino acids 69-98 of HSI1RA_P6 (SEQ IDNO:66), wherein said first amino acid sequence, second amino acidsequence and third amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P6 (SEQ IDNO:66), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) of HSI1RA_P6 (SEQ ID NO:66).

3. Comparison Report Between HSI1RA_P6 (SEQ ID NO:66) and NP_(—)776213(SEQ ID NO: 533):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P6 (SEQ IDNO:66), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) correspondingto amino acids 1-21 of HSI1RA_P6 (SEQ ID NO:66), a second amino acidsequence being at least 90% homologous toETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 25-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds toamino acids 22-68 of HSI1RA_P6 (SEQ ID NO:66), and a third amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 69-98 of HSI1RA_P6 (SEQ ID NO:66), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

4. Comparison Report Between HSI1RA_P6 (SEQ ID NO:66) and P18510-4 (SEQID NO:375)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P6 (SEQ IDNO:66), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579)corresponding to amino acids 1-34 of HSI1RA_P6 (SEQ ID NO:66), a secondamino acid sequence being at least 90% homologous toMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to amino acids 1-34 ofP18510-4 (SEQ ID NO:375), which also corresponds to amino acids 35-68 ofHSI1RA_P6 (SEQ ID NO:66), and a third amino acid sequence being at least70%, optionally at least 80%, preferably at least 85%, more preferablyat least 90% and most preferably at least 95% homologous to apolypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ IDNO: 474) corresponding to amino acids 69-98 of HSI1RA_P6 (SEQ ID NO:66),wherein said first amino acid sequence, second amino acid sequence andthird amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P6 (SEQ IDNO:66), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) of HSI1RA_P6 (SEQ IDNO:66).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSI1RA_P6 (SEQ ID NO:66) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 91,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSI1RA_P6 (SEQ ID NO:66) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 91 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 54 Q -> * 76 P -> S 77 M -> T 79 V -> L

The glycosylation sites of variant protein HSI1RA_P6 (SEQ ID NO:66), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 92 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 92 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 93:

TABLE 93 InterPro domain(s) Domain description Analysis type Position(s)on protein Interleukin-1 BlastProDom 33-68 Interleukin-1 receptorFPrintScan 34-54, 55-75 antagonist IL1RA

Variant protein HSI1RA_P6 (SEQ ID NO:66) is encoded by the followingtranscript(s): HSI1RA_T16 (SEQ ID NO:63), for which the coding portionstarts at position 376 and ends at position 669. The transcript also hasthe following SNPs as listed in Table 94 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSI1RA_P6 (SEQ IDNO:66) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 94 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> G 40, 1143, 2344, 2364, 2427 C -> T 268, 535, 601, 756,822, 1031, 1918, 2058, 2214, 2451, 2220, 2356 G -> A 304, 612, 444, 715,738, 1804, 2289, 2600, 3253 T -> C 546, 605, 712, 2145, 2188, 2599 G ->C 610, 633, 1809 G -> T 797 A -> G 1011, 1142, 1896 -> T 2062 C -> 2121,2344 T -> 2779, 2910, 2980

Variant protein HSI1RA_P13 (SEQ ID NO:67) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T13 (SEQ ID NO:62).An alignment is given to the known protein (Interleukin-1 receptorantagonist protein precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSI1RA_P13 (SEQ ID NO:67) and IL1X_HUMAN(SEQ ID NO: 372):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P13 (SEQ IDNO:67), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95% homologous to a polypeptidehaving the sequence MAL (SEQ ID NO: 580) corresponding to amino acids1-3 of HSI1RA_P13 (SEQ ID NO:67), a second amino acid sequence being atleast 90% homologous to ETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 22-68 of IL1X_HUMAN (SEQ ID NO: 372), whichalso corresponds to amino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67), and athird amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

2. Comparison Report Between HSI1RA_P13 (SEQ ID NO:67) and NP_(—)000568(SEQ ID NO: 532):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P13 (SEQ IDNO:67), comprising a first amino acid sequence being at least 90%homologous to MALETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 1-50 of NP_(—)000568 (SEQ ID NO: 532),which also corresponds to amino acids 1-50 of HSI1RA_P13 (SEQ ID NO:67),and a second amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

3. Comparison Report Between HSI1RA_P13 (SEQ ID NO:67) and P18510-3 (SEQID NO:374)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P13 (SEQ IDNO:67), comprising a first amino acid sequence being at least 90%homologous to MAL (SEQ ID NO: 580) corresponding to amino acids 1-3 ofP18510-3 (SEQ ID NO:374), which also corresponds to amino acids 1-3 ofHSI1RA_P13 (SEQ ID NO:67), a second amino acid sequence being at least90% homologous to ETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 25-71 of P18510-3 (SEQ ID NO:374), whichalso corresponds to amino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67), and athird amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHSI1RA_P13 (SEQ ID NO:67), comprising a polypeptide having a length “n”,wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise LE, having a structure as follows: asequence starting from any of amino acid numbers 3−x to 3; and ending atany of amino acid numbers 4+((n−2)−x), in which x varies from 0 to n−2.

C. An isolated polypeptide encoding for an edge portion of HSI1RA_P13(SEQ ID NO:67), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO:474) of HSI1RA_P13 (SEQ ID NO:67).

4. Comparison Report Between HSI1RA_P13 (SEQ ID NO:67) and NP_(—)776214(SEQ ID NO: 534):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P13 (SEQ IDNO:67), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95% homologous to a polypeptidehaving the sequence MAL (SEQ ID NO: 580) corresponding to amino acids1-3 of HSI1RA_P13 (SEQ ID NO:67), a second amino acid sequence being atleast 90% homologous to ETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 22-68 of NP_(—)776214 (SEQ ID NO: 534),which also corresponds to amino acids 4-50 of HSI1RA_P13 (SEQ ID NO:67),and a third amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO: 474) corresponding to aminoacids 51-80 of HSI1RA_P13 (SEQ ID NO:67), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

5. Comparison Report Between HSI1RA_P13 (SEQ ID NO:67) and P18510-4 (SEQID NO:375)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P13 (SEQ IDNO:67), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MALETICRPSGRKSSK (SEQ ID NO: 581) corresponding toamino acids 1-16 of HSI1RA_P13 (SEQ ID NO:67), a second amino acidsequence being at least 90% homologous toMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to amino acids 1-34 ofP18510-4 (SEQ ID NO:375), which also corresponds to amino acids 17-50 ofHSI1RA_P13 (SEQ ID NO:67), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ IDNO: 474) corresponding to amino acids 51-80 of HSI1RA_P13 (SEQ IDNO:67), wherein said first amino acid sequence, second amino acidsequence and third amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P13 (SEQ IDNO:67), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMALETICRPSGRKSSK (SEQ ID NO: 581) of HSI1RA_P13 (SEQ ID NO:67).

C. An isolated polypeptide encoding for an edge portion of HSI1RA_P13(SEQ ID NO:67), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEWLPGKPMYVGITSLCPSVCSSMACLHKP (SEQ ID NO:474) of HSI1RA_P13 (SEQ ID NO:67).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellularly.

Variant protein HSI1RA_P13 (SEQ ID NO:67) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table 95,(given according to their position(s) on the amino acid sequence, withthe alternative amino acid(s) listed; the presence of known SNPs invariant protein HSI1RA_P13 (SEQ ID NO:67) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 95 Amino acid mutations SNP position(s) on amino acid Alternativesequence amino acid(s) 36 Q -> * 58 P -> S 59 M -> T 61 V -> L

The glycosylation sites of variant protein HSI1RA_P13 (SEQ ID NO:67), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 96 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 96 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 97:

TABLE 97 InterPro domain(s) Domain description Analysis type Position(s)on protein Interleukin-1 BlastProDom 15-50 Interleukin-1 receptorFPrintScan 16-36, 37-57 antagonist IL1RA

Variant protein HSI1RA_P13 (SEQ ID NO:67) is encoded by the followingtranscript(s): HSI1RA_T13 (SEQ ID NO:62), for which the coding portionstarts at position 155 and ends at position 394. The transcript also hasthe following SNPs as listed in Table 98 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSI1RA_P13 (SEQ IDNO:67) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 98 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 68, 169, 337, 440, 463, 1529, 2014, 2325, 2978 A -> G124, 736, 867, 1621 G -> C 143, 335, 358, 1534 C -> T 260, 326, 481,547, 756, 1643, 1783, 1939, 1945, 2081, 2176 T -> C 271, 330, 437, 1870,1913, 2324 T -> G 399, 2533, 2641 A -> C 402, 574, 1199, 1988, 2398 C ->A 413, 784, 868, 1198 G -> T 522 C -> G 868, 2069, 2089, 2152 -> T 1787C -> 1846, 2069 T -> 2504, 2635, 2705

Variant protein HSI1RA_P14 (SEQ ID NO:68) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T2 (SEQ ID NO:61). Analignment is given to the known protein (Interleukin-1 receptorantagonist protein precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSI1RA_P14 (SEQ ID NO:68) and NP_(—)776213(SEQ ID NO: 533):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P14 (SEQ IDNO:68), comprising a first amino acid sequence being at least 90%homologous to MALADLYEEGGGGGGEGEDNADSK corresponding to amino acids 1-24of NP_(—)776213 (SEQ ID NO: 533), which also corresponds to amino acids1-24 of HSI1RA_P14 (SEQ ID NO:68), and a second amino acid sequencebeing at least 70%, optionally at least 80%, preferably at least 85%,more preferably at least 90% and most preferably at least 95% homologousto a polypeptide having the sequence GGL (SEQ ID NO: 477) correspondingto amino acids 25-27 of HSI1RA_P14 (SEQ ID NO:68), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P14(SEQ ID NO:68), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GGL (SEQ ID NO: 477) of HSI1RA_P14 (SEQ IDNO:68).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HSI1RA_P14 (SEQ ID NO:68), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 99 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 99 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

Variant protein HSI1RA_P14 (SEQ ID NO:68) is encoded by the followingtranscript(s): HSI1RA_T2 (SEQ ID NO:61), for which the coding portionstarts at position 155 and ends at position 235. The transcript also hasthe following SNPs as listed in Table 100 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSI1RA_P14 (SEQ IDNO:68) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 100 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 68, 386, 403, 868, 1179, 1832 A -> G 124 G -> C 143 C ->T 494, 637, 793, 799, 935, 1030 T -> C 505, 724, 767, 1178 -> T 641 C ->700, 923 A -> C 842, 1252 C -> G 923, 943, 1006 T -> 1358, 1489, 1559 T-> G 1387, 1495

Variant protein HSI1RA_P16 (SEQ ID NO:69) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T19 (SEQ ID NO:64).An alignment is given to the known protein (Interleukin-1 receptorantagonist protein precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSI1RA_P16 (SEQ ID NO:69) and IL1X_HUMAN(SEQ ID NO: 372):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P16 (SEQ IDNO:69), comprising a first amino acid sequence being at least 90%homologous toMEICRGLRSHLITLLLFLFHSETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEcorresponding to amino acids 1-68 of IL1X_HUMAN (SEQ ID NO: 372), whichalso corresponds to amino acids 1-68 of HSI1RA_P16 (SEQ ID NO:69), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceDRCGTH (SEQ ID NO: 478) corresponding to amino acids 69-74 of HSI1RA_P16(SEQ ID NO:69), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P16(SEQ ID NO:69), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence DRCGTH (SEQ ID NO: 478) of HSI1RA_P16 (SEQ IDNO:69).

2. Comparison Report Between HSI1RA_P16 (SEQ ID NO:69) and P18510-2 (SEQID NO:373)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P16 (SEQ IDNO:69), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) correspondingto amino acids 1-21 of HSI1RA_P16 (SEQ ID NO:69), a second amino acidsequence being at least 90% homologous toETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 4-50 of P18510-2 (SEQ ID NO:373), which also corresponds to aminoacids 22-68 of HSI1RA_P16 (SEQ ID NO:69), and a third amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), whereinsaid first amino acid sequence, second amino acid sequence and thirdamino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P16 (SEQ IDNO:69), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) of HSI1RA_P16 (SEQ ID NO:69).

C. An isolated polypeptide encoding for an edge portion of HSI1RA_P16(SEQ ID NO:69), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence DRCGTH (SEQ ID NO: 478) of HSI1RA_P16 (SEQ IDNO:69).

4. Comparison Report Between HSI1RA_P16 (SEQ ID NO:69) and NP_(—)776213(SEQ ID NO: 533):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P16 (SEQ IDNO:69), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) correspondingto amino acids 1-21 of HSI1RA_P16 (SEQ ID NO:69), a second amino acidsequence being at least 90% homologous toETICRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 25-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds toamino acids 22-68 of HSI1RA_P16 (SEQ ID NO:69), and a third amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), whereinsaid first amino acid sequence, second amino acid sequence and thirdamino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P16 (SEQ IDNO:69), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHS (SEQ ID NO: 578) of HSI1RA_P16 (SEQ ID NO:69).

5. Comparison Report Between HSI1RA_P16 (SEQ ID NO:69) and P18510-4 (SEQID NO:375)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P16 (SEQ IDNO:69), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579)corresponding to amino acids 1-34 of HSI1RA_P16 (SEQ ID NO:69), a secondamino acid sequence being at least 90% homologous toMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to amino acids 1-34 ofP18510-4 (SEQ ID NO:375), which also corresponds to amino acids 35-68 ofHSI1RA_P16 (SEQ ID NO:69), and a third amino acid sequence being atleast 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequence DRCGTH (SEQ ID NO: 478) corresponding toamino acids 69-74 of HSI1RA_P16 (SEQ ID NO:69), wherein said first aminoacid sequence, second amino acid sequence and third amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HSI1RA_P16 (SEQ IDNO:69), comprising a polypeptide being at least 70%, optionally at leastabout 80%, preferably at least about 85%, more preferably at least about90% and most preferably at least about 95% homologous to the sequenceMEICRGLRSHLITLLLFLFHSETICRPSGRKSSK (SEQ ID NO: 579) of HSI1RA_P16 (SEQID NO:69).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HSI1RA_P16 (SEQ ID NO:69) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table101, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HSI1RA_P16 (SEQ ID NO:69) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 101 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 54 Q -> *

The glycosylation sites of variant protein HSI1RA_P16 (SEQ ID NO:69), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 102 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 102 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 103:

TABLE 103 InterPro domain(s) Domain description Analysis typePosition(s) on protein Interleukin-1 BlastProDom 33-70 Interleukin-1receptor FPrintScan 34-54, 55-74 antagonist IL1RA

Variant protein HSI1RA_P16 (SEQ ID NO:69) is encoded by the followingtranscript(s): HSI1RA_T19 (SEQ ID NO:64), for which the coding portionstarts at position 376 and ends at position 597. The transcript also hasthe following SNPs as listed in Table 104 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSI1RA_P16 (SEQ IDNO:69) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 104 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> G 40, 959, 979, 1042 C -> T 268, 535, 673, 829, 835, 1066,971 G -> A 304, 444, 904, 1215, 1868 T -> C 546, 760, 803, 1214 -> T 677C -> 736, 959 A -> C 878, 1288 T -> 1394, 1525, 1595 T -> G 1423, 1531

Variant protein HSI1RA_P17 (SEQ ID NO:70) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSI1RA_T19 (SEQ ID NO:64).An alignment is given to the known protein (Interleukin-1 receptorantagonist protein precursor) in the alignment table on the attachedCD-ROM. A brief description of the relationship of the variant proteinaccording to the present invention to each such aligned protein is asfollows:

1. Comparison Report Between HSI1RA_P17 (SEQ ID NO:70) and IL1X_HUMAN(SEQ ID NO: 372):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P17 (SEQ IDNO:70), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 35-68 of IL1X_HUMAN (SEQ ID NO: 372), which also corresponds toamino acids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid, first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHSI1RA_P17 (SEQ ID NO:70), comprising a polypeptide having a length “n”,wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise M, having a structure as follows: asequence starting from any of amino acid numbers 1−x to 1; and ending atany of amino acid numbers 1+((n−2)−x), in which x varies from 0 to n−2.

C. An isolated polypeptide encoding for an edge portion of HSI1RA_P17(SEQ ID NO:70), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence DRCGTH (SEQ ID NO: 478) of HSI1RA_P17 (SEQ IDNO:70).

2. Comparison Report Between HSI1RA_P17 (SEQ ID NO:70) and P18510-4 (SEQID NO:375)

A. An isolated chimeric polypeptide as set forth in HSI1RA_P17 (SEQ IDNO:70), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 1-34 of P18510-4 (SEQ ID NO:375), which also corresponds to aminoacids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HSI1RA_P17(SEQ ID NO:70), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence DRCGTH (SEQ ID NO: 478) of HSI1RA_P17 (SEQ IDNO:70).

3. Comparison Report Between HSI1RA_P17 (SEQ ID NO:70) and NP_(—)000568(SEQ ID NO: 532):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P17 (SEQ IDNO:70), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 17-50 of NP_(—)000568 (SEQ ID NO: 532), which also corresponds toamino acids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

5. Comparison Report Between HSI1RA_P17 (SEQ ID NO:70) and NP_(—)776214(SEQ ID NO: 534):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P17 (SEQ IDNO:70), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 35-68 of NP_(—)776214 (SEQ ID NO: 534), which also corresponds toamino acids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

6. Comparison Report Between HSI1RA_P17 (SEQ ID NO:70) and NP_(—)776213(SEQ ID NO: 533):

A. An isolated chimeric polypeptide as set forth in HSI1RA_P17 (SEQ IDNO:70), comprising a first amino acid sequence being at least 90%homologous to MQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLE corresponding to aminoacids 38-71 of NP_(—)776213 (SEQ ID NO: 533), which also corresponds toamino acids 1-34 of HSI1RA_P17 (SEQ ID NO:70), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence DRCGTH (SEQ ID NO: 478)corresponding to amino acids 35-40 of HSI1RA_P17 (SEQ ID NO:70), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellularly.

Variant protein HSI1RA_P17 (SEQ ID NO:70) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table105, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HSI1RA_P17 (SEQ ID NO:70) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 105 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 20 Q -> *

The glycosylation sites of variant protein HSI1RA_P17 (SEQ ID NO:70), ascompared to the known protein Interleukin-1 receptor antagonist proteinprecursor, are described in Table 106 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 106 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 109No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 107:

TABLE 107 InterPro domain(s) Domain description Analysis typePosition(s) on protein Interleukin-1 BlastProDom 1-36

Variant protein HSI1RA_P17 (SEQ ID NO:70) is encoded by the followingtranscript(s): HSI1RA_T19 (SEQ ID NO:64), for which the coding portionstarts at position 478 and ends at position 597. The transcript also hasthe following SNPs as listed in Table 108 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSI1RA_P17 (SEQ IDNO:70) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 108 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> G 40, 959, 979, 1042 C -> T 268, 535, 673, 829, 835, 971,1066 G -> A 304, 444, 904, 1215, 1868 T -> C 546, 760, 736, 803, 1214 ->T 677 C -> 736, 959 A -> C 878, 1288 T -> 1394, 1595, 1525 T -> G 1423,1531

As noted above, cluster HSI1RA features 25 segment(s), which were listedin Table 83 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segments 15, 17, 23, 24, 30, 36, and 37 according to the presentinvention is now provided.

Segment cluster HSI1RA_N17 (SEQ ID NO:73) according to the presentinvention is supported by 10 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T2 (SEQ ID NO:61). Table 109 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 109 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T2 (SEQ ID NO: 61) 228 398

Segment cluster HSI1RA_N24 (SEQ ID NO:78) according to the presentinvention is supported by 11 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T13 (SEQ ID NO:62) and HSI1RA_T16 (SEQID NO:63). Table 110 below describes the starting and ending position ofthis segment on each transcript.

TABLE 110 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T13 (SEQ ID NO: 62) 3061203 HSI1RA_T16 (SEQ ID NO: 63) 581 1478

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster HSI1RA_N15 (SEQ ID NO:72) according to the presentinvention is supported by 7 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T2 (SEQ ID NO:61). Table 111 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 111 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T2 (SEQ ID NO: 61) 165 227

Segment cluster HSI1RA_N23 (SEQ ID NO:77) according to the presentinvention is supported by 104 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T13 (SEQ ID NO:62), HSI1RA_T16 (SEQ IDNO:63), HSI1RA_T19 (SEQ ID NO:64) and HSI1RA_T2 (SEQ ID NO:61). Table112 below describes the starting and ending position of this segment oneach transcript.

TABLE 112 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T13 (SEQ ID NO: 62) 217305 HSI1RA_T16 (SEQ ID NO: 63) 492 580 HSI1RA_T19 (SEQ ID NO: 64) 492580 HSI1RA_T2 (SEQ ID NO: 61) 451 539

Segment cluster HSI1RA_N30 (SEQ ID NO:84) according to the presentinvention is supported by 110 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T13 (SEQ ID NO:62), HSI1RA_T16 (SEQ IDNO:63), HSI1RA_T19 (SEQ ID NO:64) and HSI1RA_T2 (SEQ ID NO:61). Table113 below describes the starting and ending position of this segment oneach transcript.

TABLE 113 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T13 (SEQ ID NO: 62) 16911792 HSI1RA_T16 (SEQ ID NO: 63) 1966 2067 HSI1RA_T19 (SEQ ID NO: 64) 581682 HSI1RA_T2 (SEQ ID NO: 61) 545 646

Segment cluster HSI1RA_N36 (SEQ ID NO:87) according to the presentinvention is supported by 108 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T13 (SEQ ID NO:62), HSI1RA_T16 (SEQ IDNO:63), HSI1RA_T19 (SEQ ID NO:64) and HSI1RA_T2 (SEQ ID NO:61). Table114 below describes the starting and ending position of this segment oneach transcript.

TABLE 114 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T13 (SEQ ID NO: 62) 18031878 HSI1RA_T16 (SEQ ID NO: 63) 2078 2153 HSI1RA_T19 (SEQ ID NO: 64) 693768 HSI1RA_T2 (SEQ ID NO: 61) 657 732

Segment cluster HSI1RA_N37 (SEQ ID NO:88) according to the presentinvention is supported by 105 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSI1RA_T13 (SEQ ID NO:62), HSI1RA_T16 (SEQ IDNO:63), HSI1RA_T19 (SEQ ID NO:64) and HSI1RA_T2 (SEQ ID NO:61). Table115 below describes the starting and ending position of this segment oneach transcript.

TABLE 115 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSI1RA_T13 (SEQ ID NO: 62) 18791956 HSI1RA_T16 (SEQ ID NO: 63) 2154 2231 HSI1RA_T19 (SEQ ID NO: 64) 769846 HSI1RA_T2 (SEQ ID NO: 61) 733 810FIG. 6 shows the structure of the HSI1RA mRNA and protein variants Exonsare represented by white boxes, while introns are represented by twoheaded arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe. Expression of Homo sapiens interleukin 1 receptor antagonist(IL1RN) HSI1RA transcripts which are detectable by amplicon as depictedin sequence name HSI1RA_junc15-17 (SEQ ID NO:376) in normal andcancerous Lung tissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to junc15-17—HSI1RA_junc15-17(SEQ ID NO:376) amplicon and primers HSI1RA_junc15-17F (SEQ ID NO:377)and HSI1RA_junc15-17R (SEQ ID NO:378) was measured by real time PCR. Inparallel the expression of four housekeeping genes—HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)), SDHA (GenBank Accession No.NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ ID NO:365))and Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers47, 48, 49, 50, 91, 92, 93, 96, 97 and 98, Table 3 above), to obtain avalue of fold up-regulation for each sample relative to median of thenormal PM samples.

FIG. 7 is a histogram showing over expression of the above-indicatedHomo sapiens interleukin 1 receptor antagonist (IL1RN) transcripts incancerous Lung samples relative to the normal samples.

As is evident from FIG. 7, the expression of Homo sapiens interleukin 1receptor antagonist (IL1RN) transcripts detectable by the above ampliconin squamous cell carcinoma, large cell carcinoma and non-small cellcarcinoma samples was higher than in the non-cancerous samples (samplenumbers 47, 48, 49, 50, 91, 92, 93, 96, 97 and 98, Table 3 above).Notably an over-expression of at least 5 fold was found in 7 out of 16squamous cell carcinoma samples, in 2 out of 3 large cell carcinomasamples and in 11 out of 32 non-small cell carcinoma samples. Inaddition the expression of Homo sapiens interleukin 1 receptorantagonist (IL1RN) transcripts detectable by the above amplicon in smallcell carcinoma samples was lower than in the non-cancerous samples(sample numbers 47, 48, 49, 50, 91, 92, 93, 96, 97 and 98, Table 3above).

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSI1RA_junc15-17F (SEQ ID NO:377) forward primer;and HSI1RA_junc15-17R (SEQ ID NO:378) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSI1RA_junc15-17 (SEQID NO:376).

Forward Primer (HSI1RA_junc15-17F (SEQ ID NO: 377)): TGCTGACTCAAAGGGGGGAReverse Primer (HSI1RA_junc15-17R (SEQ ID NO: 378)):CCAGCAGTTTATGGGTTAGCTATG Amplicon (HSI1RA_junc15-17 (SEQ ID NO:376)):TGCTGACTCAAAGGGGGGATTATAAAACTAATCATCAAAGCCAAGAAGGCAAGAGCAAGCATGTACCGCTGAAAACACAAGATAACTGCATAAGTAATGACTTTCAGTGCAGATTCATAGCTAACCCATAAACTGCTGGExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA_junc15-17 (SEQ ID NO:376) in Different NormalTissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to junc15-17—HSI1RA_junc15-17(SEQ ID NO:376) amplicon and primers HSI1RA_junc15-17F (SEQ ID NO:377)and HSI1RA_junc15-17R (SEQ ID NO:378) was measured by real time PCR. Inparallel the expression of four housekeeping genes—SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (GenBank AccessionNo. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon) andTATA box (GenBank Accession No. NM_(—)003194 (SEQ ID NO:371); TATA (SEQID NO:370) amplicon) was measured similarly. For each RT sample, theexpression of the above amplicon was normalized to the geometric mean ofthe quantities of the housekeeping genes. The normalized quantity ofeach RT sample was then divided by the median of the quantities of theesophagus samples (sample numbers 11 and 12, Table 5 above), to obtain avalue of relative expression of each sample relative to median of theesophagus samples. FIG. 8 shows expression of Homo sapiens interleukin 1receptor antagonist (IL1RN) HSI1RA transcripts which are detectable byamplicon as depicted in sequence name HSI1RA_junc15-17 (SEQ ID NO:376)in different normal tissues.

Forward Primer (HSI1RA_junc15-17F (SEQ ID NO: 377)): TGCTGACTCAAAGGGGGGAReverse Primer (HSI1RA_junc15-17R (SEQ ID NO: 378)):CCAGCAGTTTATGGGTTAGCTATG Amplicon HSI1RA_junc15-17 (SEQ ID NO:376):TGCTGACTCAAAGGGGGGATTATAAAACTAATCATCAAAGCCAAGAAGGCAAGAGCAAGCATGTACCGCTGAAAACACAAGATAACTGCATAAGTAATGACTTTCAGTGCAGATTCATAGCTAACCCATAAACTGCTGGExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA_junc23-30 (SEQ ID NO: 383) in Normal and CancerousLung Tissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to junc23-30, HSI1RA junc23-30(SEQ ID NO: 383) amplicon and primers HSI1RA junc23-30F (SEQ ID NO: 384)and HSI1RA junc23-30R (SEQ ID NO: 385) was measured by real time PCR. Inparallel the expression of four housekeeping genes —PBGD (GenBankAccession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ IDNO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO: 379);amplicon—HPRT1-amplicon (SEQ ID NO:380)), Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (Sample Nos.47-50, 90-93, 96-99, Table 3), to obtain a value of fold differentialexpression for each sample relative to median of the normal PM samples.

FIG. 9 is a histogram showing down regulation of the above-indicatedHomo sapiens interleukin 1 receptor antagonist (IL1RN) transcripts incancerous lung samples relative to the normal samples (junc23-30).

As is evident from FIG. 9, the expression of Homo sapiens interleukin 1receptor antagonist (IL1RN) transcripts detectable by the above ampliconin small cell carcinoma samples was lower than in the non-canceroussamples (Sample Nos. 46-50, 90-93, 96-99 Table 3).

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSI1RA junc23-30F (SEQ ID NO: 384) forward primer;and HSI1RA junc23-30R (SEQ ID NO: 385) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSI1RA_junc23-30 (SEQID NO: 383).

Forward primer HSI1RA_junc23-30F (SEQ ID NO: 384):AGGACCAAATGTCAATTTAGAAGATAGA Reverse primer HSI1RA_junc23-30R (SEQ IDNO: 385): GACTTGACACAGGACAGGCACA Amplicon HSI1RA junc23-30 (SEQ ID NO:383): AGGACCAAATGTCAATTTAGAAGATAGATGTGGTACCCATTGAGCCTCATGCTCTGTTCTTGGGAATCCATGGAGGGAAGATGTGCCTGTCCTGTGTCAA GTCExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA_junc23-30 (SEQ ID NO: 383) in Different NormalTissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to junc23-30—HSI1RA_junc23-30(SEQ ID NO: 383) amplicon and primers HSI1RA_junc23-30F (SEQ ID NO: 384)and HSI1RA_junc23-30R (SEQ ID NO: 385) was measured by real time PCR. Inparallel the expression of four housekeeping genes—SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (GenBank AccessionNo. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon) andTATA box (GenBank Accession No. NM_(—)003194 (SEQ ID NO:371); TATA (SEQID NO:370) amplicon) was measured similarly. For each RT sample, theexpression of the above amplicon was normalized to the geometric mean ofthe quantities of the housekeeping genes. The normalized quantity ofeach RT sample was then divided by the median of the quantities of theesophagus samples (sample numbers 11 and 12, Table 5 above), to obtain avalue of relative expression of each sample relative to median of theesophagus samples. FIG. 10 shows expression of Homo sapiens interleukin1 receptor antagonist (IL1RN) HSI1RA transcripts which are detectable byamplicon as depicted in sequence name HSI1RA_junc23-30 (SEQ ID NO: 383)in different normal tissues.

Forward Primer (HSI1RA_junc23-30F (SEQ ID NO: 384)):AGGACCAAATGTCAATTTAGAAGATAGA Reverse Primer (HSI1RA_junc23-30R (SEQ IDNO: 385)): GACTTGACACAGGACAGGCACA Amplicon HSI1RA_junc23-30 (SEQ ID NO:383): AGGACCAAATGTCAATTTAGAAGATAGATGTGGTACCCATTGAGCCTCATGCTCTGTTCTTGGGAATCCATGGAGGGAAGATGTGCCTGTCCTGTGTCAA GTCExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA seg23-24 (SEQ ID NO: 386) in Normal and CancerousLung Tissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to seg23-24, HSI1RA seg23-24 (SEQID NO: 386) amplicon and primers HSI1RA seg23-24F (SEQ ID NO: 387) andHSI1RA seg23-24R (SEQ ID NO: 388) was measured by real time PCR. Inparallel the expression of four housekeeping genes —PBGD (GenBankAccession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ IDNO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO: 379);amplicon—HPRT1-amplicon (SEQ ID NO:380)), Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples, for which thevalues are presented in FIG. 10A (Sample Nos. 47-50, 90-93, 96-99, Table3, above). Then the reciprocal of this ratio was calculated, to obtain avalue of fold down-regulation for each sample relative to median of thenormal PM samples for which values are presented in FIG. 11B.

FIGS. 11A and 11B are histograms showing down regulation of theabove-indicated Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts in cancerous lung samples relative to the normal samples(seg 23-24).

As is evident from FIGS. 11A and 11B, the expression of Homo sapiensinterleukin 1 receptor antagonist (IL1RN) transcripts detectable by theabove amplicon in small cell carcinoma samples was significantly lowerthan in the non-cancerous samples (Sample Nos. 46-50, 90-93, 96-99 Table3). Notably down regulation of at least 5 fold was found in 7 out of 8small cells carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapiensinterleukin 1 receptor antagonist (IL1RN) transcripts detectable by theabove amplicon in lung cancer samples versus the normal tissue sampleswas determined by T test as 5.02E-02.

Threshold of 5 fold down regulation was found to differentiate betweencancer and normal samples with P value of 2.49E-02 as checked by exactfisher test. The above values demonstrate statistical significance ofthe results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSI1RA seg23-24F (SEQ ID NO: 387) forward primer;and HSI1RA seg23-24R (SEQ ID NO: 388) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSI1RA seg23-24 (SEQID NO: 386).

Forward primer HSI1RA seg23-24F (SEQ ID NO: 387):CAACCAACTAGTTGCTGGATACTTG Reverse primer HSI1RA seg23-24R (SEQ ID NO:388): GGCAAAGTGACGTGATGCC Amplicon HSI1RA seg23-24 (SEQ ID NO: 386):CAACCAACTAGTTGCTGGATACTTGCAAGGACCAAATGTCAATTTAGAAGGTGAGTGGTTGCCAGGAAAGCCAATGTATGTGGGCATCACGTCACTTTGC CExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA_seg23-24 (SEQ ID NO: 386) in Different NormalTissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to seg23-24—HSI1RA_seg23-24 (SEQID NO: 386) amplicon and primers HSI1RA_seg23-24F (SEQ ID NO: 387) andHSI1RA_seg23-24R (SEQ ID NO: 388) was measured by real time PCR. Inparallel the expression of four housekeeping genes—SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (GenBank AccessionNo. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon) andTATA box (GenBank Accession No. NM_(—)003194 (SEQ ID NO:371); TATA (SEQID NO:370) amplicon) was measured similarly. For each RT sample, theexpression of the above amplicon was normalized to the geometric mean ofthe quantities of the housekeeping genes. The normalized quantity ofeach RT sample was then divided by the median of the quantities of theesophagus samples (sample numbers 11 and 12, Table 5 above), to obtain avalue of relative expression of each sample relative to median of theesophagus samples. FIG. 12 shows expression of Homo sapiens interleukin1 receptor antagonist (IL1RN) HSI1RA transcripts which are detectable byamplicon as depicted in sequence name HSI1RA_seg23-24 (SEQ ID NO: 386)in different normal tissues.

Forward primer (HSI1RA_seg23-24F (SEQ ID NO: 387)):CAACCAACTAGTTGCTGGATACTTG Reverse primer (HSI1RA_seg23-24R (SEQ ID NO:388)): GGCAAAGTGACGTGATGCC Amplicon HSI1RA_seg23-24 (SEQ ID NO: 386):CAACCAACTAGTTGCTGGATACTTGCAAGGACCAAATGTCAATTTAGAAGGTGAGTGGTTGCCAGGAAAGCCAATGTATGTGGGCATCACGTCACTTTGC CExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA seg36-37WT (SEQ ID NO: 389) in Normal and CancerousLung Tissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to seg36-37, HSI1RA seg36-37WT(SEQ ID NO: 389) amplicon and primers HSI1RA seg36-37WTF (SEQ ID NO:390) and HSI1RA seg36-37WTR (SEQ ID NO: 391) was measured by real timePCR. In parallel the expression of four housekeeping genes —PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), was measuredsimilarly. For each RT sample, the expression of the above amplicon wasnormalized to the geometric mean of the quantities of the housekeepinggenes. The normalized quantity of each RT sample was then divided by themedian of the quantities of the normal post-mortem (PM) samples forwhich values presented in FIG. 13A (Sample Nos. 47-50, 90-93, 96-99,Table 3, above). Then the reciprocal of this ratio was calculated, toobtain a value of fold down-regulation for each sample relative tomedian of the normal PM samples for which values are presented in FIG.13B.

FIGS. 13A and 13B are histograms showing down regulation of theabove-indicated Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts in cancerous lung samples relative to the normal samples(seg 36-37).

As is evident from FIGS. 12A and 12B, the expression of Homo sapiensinterleukin 1 receptor antagonist (IL1RN) transcripts detectable by theabove amplicon in small cell carcinoma samples was significantly lowerthan in the non-cancerous samples (Sample Nos. 46-50, 90-93, 96-99 Table3). Notably down regulation of at least 5 fold was found in 8 out of 8small cells carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

Threshold of 5 fold down regulation was found to differentiate betweensmall cell carcinoma and normal samples with P value of 7.94E-06 aschecked by exact fisher test. The above values demonstrate statisticalsignificance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSI1RA seg36-37WTF (SEQ ID NO: 390) forwardprimer; and HSI1RA seg36-37WTR (SEQ ID NO: 391) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSI1RA seg36-37WT (SEQID NO: 389).

Forward primer HSI1RA seg36-37WTF (SEQ ID NO: 390):GAGCGAGAACAGAAAGCAGGA Reverse primer HSI1RA seg36-37WTR (SEQ ID NO:391): GCTGTGCAGAGGAACCAACC Amplicon HSI1RA seg36-37WT (SEQ ID NO: 389):GAGCGAGAACAGAAAGCAGGACAAGCGCTTCGCCTTCATCCGCTCAGACAGTGGCCCCACCACCAGTTTTGAGTCTGCCGCCTGCCCCGGTTGGTTCCTC TGCACAGCExpression of Homo sapiens Interleukin 1 Receptor Antagonist (IL1RN)HSI1RA Transcripts which are Detectable by Amplicon as Depicted inSequence Name HSI1RA_seg36-37WT (SEQ ID NO: 389) in Different NormalTissues

Expression of Homo sapiens interleukin 1 receptor antagonist (IL1RN)transcripts detectable by or according to seg36-37WT—HSI1RA_seg36-37WT(SEQ ID NO: 389) amplicon and primers HSI1RA_seg36-37WTF (SEQ ID NO:390) and HSI1RA_seg36-37WTR (SEQ ID NO: 391) was measured by real timePCR. In parallel the expression of four housekeeping genes—SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (GenBank AccessionNo. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon) andTATA box (GenBank Accession No. NM_(—)003194 (SEQ ID NO:371); TATA (SEQID NO:370) amplicon) was measured similarly. For each RT sample, theexpression of the above amplicon was normalized to the geometric mean ofthe quantities of the housekeeping genes. The normalized quantity ofeach RT sample was then divided by the median of the quantities of theesophagus samples (sample numbers 11 and 12, Table 5 above), to obtain avalue of relative expression of each sample relative to median of theesophagus samples. FIG. 14 shows expression of Homo sapiens interleukin1 receptor antagonist (IL1RN) HSI1RA transcripts which are detectable byamplicon as depicted in sequence name HSI1RA_seg36-37WT (SEQ ID NO: 389)in different normal tissues.

Forward Primer (HSI1RA_seg36-37WTF (SEQ ID NO: 390)):GAGCGAGAACAGAAAGCAGGA Reverse Primer (HSI1RA_seg36-37WTR (SEQ ID NO:391)): GCTGTGCAGAGGAACCAACC Amplicon HSI1RA_seg36-37WT (SEQ ID NO: 389):GAGCGAGAACAGAAAGCAGGACAAGCGCTTCGCCTTCATCCGCTCAGACAGTGGCCCCACCACCAGTTTTGAGTCTGCCGCCTGCCCCGGTTGGTTCCTC TGCACAGC

Description for Cluster HSPLGF

Cluster HSPLGF features 3 transcript(s) and 11 segment(s) of interest,the names for which are given in Tables 116 and 117, respectively. Theselected protein variants are given in table 118.

TABLE 116 Transcripts of interest Transcript name HSPLGF_1_T2 (SEQ IDNO: 96) HSPLGF_1_T6 (SEQ ID NO: 97) HSPLGF_1_T15 (SEQ ID NO: 98)

TABLE 117 Segments of interest Segment Name HSPLGF_1_N0 (SEQ ID NO: 103)HSPLGF_1_N2 (SEQ ID NO: 104) HSPLGF_1_N7 (SEQ ID NO: 107) HSPLGF_1_N21(SEQ ID NO: 113) HSPLGF_1_N3 (SEQ ID NO: 105) HSPLGF_1_N4 (SEQ ID NO:106) HSPLGF_1_N9 (SEQ ID NO: 108) HSPLGF_1_N14 (SEQ ID NO: 109)HSPLGF_1_N15 (SEQ ID NO: 110) HSPLGF_1_N16 (SEQ ID NO: 111) HSPLGF_1_N17(SEQ ID NO: 112)

TABLE 118 Proteins of interest Protein Name Corresponding Transcript(s)HSPLGF_1_P4 (SEQ ID NO: 99) HSPLGF_1_T2 (SEQ ID NO: 96) HSPLGF_1_P5 (SEQID NO: 100) HSPLGF_1_T6 (SEQ ID NO: 97) HSPLGF_1_P13 (SEQ ID NO: 101)HSPLGF_1_T15 (SEQ ID NO: 98) HSPLGF_1_P14 (SEQ ID NO: 102) HSPLGF_1_T6(SEQ ID NO: 97)

These sequences are variants of the known protein Placenta growth factorprecursor (SwissProt accession identifier PLGF_HUMAN (SEQ ID NO:392);known also according to the synonyms PlGF), referred to herein as thepreviously known protein.

Protein Placenta growth factor precursor is known or believed to havethe following function(s): Growth factor active in angiogenesis, andendothelial cell growth, stimulating their proliferation and migration.It binds to receptor VEGFR-1/FLT1. PLGF-2 binds neuropilin-1 and 2 in aheparin-dependent manner. Known polymorphisms for this sequence are asshown in Table 119.

TABLE 119 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 91 N -> D

Protein Placenta growth factor precursor localization is believed to besecreted but PlGF-2 form appears to remain cell attached unless releasedby heparin.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: cell-cell signaling; positiveregulation of cell proliferation; signal transduction, which areannotation(s) related to Biological Process; and growth factor activity,which are annotation(s) related to Molecular Function.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

According to optional embodiments of the present invention, variants ofthis cluster according to the present invention (amino acid and/ornucleic acid sequences of HSPLGF) may optionally have one or more of thefollowing utilities, as described with regard to the Table below. Itshould be noted that these utilities are optionally and preferablysuitable for human and non-human animals as subjects, except whereotherwise noted. The reasoning is described with regard to biologicaland/or physiological and/or other information about the known protein,but is given to demonstrate particular diagnostic utility for thevariants according to the present invention.

HSPLGF placental growth factor, a member of the vascular endothelialgrowth factor (VEGF) family, is a molecular marker for inflammation.Upregulation of placental growth factor has been found in severalconditions associated with pathological angiogenesis and monocyterecruitment that underlie chronic inflammatory disease. In patients withacute chest pain, a high blood level of placental growth factor predictsa poor prognosis.

TABLE 120 Utilities for Variants of HSPLGF, related to placental growthfactor: Dx field Explanation Ref Inflammation Chronic transgenicdelivery of Blood First Edition Paper on Marker for Crohn's disease andPlGF-2 to murine epidermis Sep. 5, 2002; DOI ulcerative colitis patientsin resulted in a significantly 10.1182/blood-2002-05-1516 remissionversus active disease increased inflammatory response, Am JGastroenterol. 2005 associated with more pronounced Feb; 100(2): 414-23vascular enlargement, edema, and inflammatory cell infiltration thanseen in wild-type mice. Conversely, PlGF deficiency resulted in adiminished and abbreviated inflammatory response, together with areduction of inflammatory angiogenesis and edema formation. Proteinmicroarray analysis of disease activity in pediatric inflammatory boweldisease demonstrates elevated serum PLGF levels in Crohn's disease andulcerative colitis patients in remission versus active diseasePrognostic Value of in Patients In patients with ACS, elevated JAMA.2004; 291: 435-441 With Acute Chest Pain PlGF levels indicated amarkedly Clin Chem. 2005 May; 51(5): 810-24. (predicting ACS) increasedrisk for death or Epub 2005 Mar 17. Biomarker for detection of nonfatalmyocardial infarction ischemia and risk stratification in after 30 days.It acts as a primary acute coronary syndrome inflammatory instigator ofatherosclerotic plaque instability and thus may be useful as a risk-predicting biomarker in patients with acute coronary syndromes (ACS).Prediction of preeclampsia in the A decreased maternal serum Obstetrics& Gynecology early second trimester of placenta growth factor 2001; 97:898-904 pregnancy concentration in the early second Int J GynaecolObstet. 2005 trimester is highly associated with Jun; 89(3): 251-7. Epub2005 Apr the subsequent development of 2. preeclampsia PredictsCardiovascular Elevated Placental Growth Factor Scand J Clin Lab InvestSuppl. Morbidity and Mortality in Type (PlGF) Predicts Cardiovascular2005; 240: 73-9. 1 Diabetic Patients with Diabetic Morbidity andMortality in Type Nephropathy. 1 Diabetic Patients with DiabeticNephropathy. Marker for survival of patients The majority of PIGF wasGut. 2005 May; 54(5): 666-72. with colorectal cancer expressed in tumourcells. The ratio of PIGF expression in tumour to non-tumour in theadvanced disease group was significantly higher than for the localiseddisease group (p = 0.009). Patients with more tumour PlGF mRNA hadshorter survival (p = 0.028). Marker for gastric cancer PlGF expressionlevel was Cancer Lett. 2004 Sep diagnosis, staging and gradingsignificantly correlated with 15; 213(1): 73-82. serosal invasion,positive lymph node metastases, tumor stages, and patient survival.Marker for grading and tumor PlGF and VEGF levels in patients AnticancerRes. 2003 Nov- vasculrity assessment as with RCC were significantly Dec;23(6D): 4953-8. prognostic factors in renal cell higher than those innon-cancer cancer (RCC), - as a stand alone controls. PlGF levels weremarker or in combination with significantly associated with VEGFhistological grade and total tumor vascularity (TTV), and VEGF levelswere significantly associated with T, M stage, histological grade,venous invasion and TTV. Multivariate analysis showed plasma PlGF was anindependent prognostic factor. These findings suggested that plasma PlGFlevels were significantly associated with the clinical features of RCC,especially prognostic significance.

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HSPLGF) may optionally have one or moreof the following utilities, some of which are related to utilitiesdescribed above. It should be noted that these utilities are optionallyand preferably suitable for human and non-human animals as subjects,except where otherwise noted.

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HSPLGF) may optionally have one or moreof the following utilities: used as surrogate markers, that should bemeasured in subjects undergoing various treatments of diseases such asChronic inflammation and ACS.

Treatments for chronic inflammation using, for example, COX1 and COX2inhibitors, Steroids, TNF blockers (like Humira); and treatments for ACSthrombolysis (e.g. tPA, streptokinase), aspirin, or catheterization mayaffect the level of variants of HSPLGF cluster according to the presentinvention (amino acid and/or nucleic acid sequences of HSPLGF) andtherefore it may serve as surrogate marker.

Other non-limiting exemplary utilities for HSPLGF variants according tothe present invention are described in greater detail below and alsowith regard to the previous section on clinical utility.

As noted above, cluster HSPLGF features 3 transcript(s), which werelisted in Table 116 above. These transcript(s) encode for protein(s)which are variant(s) of protein Placenta growth factor precursor. Adescription of each variant protein according to the present inventionis now provided.

Variant protein HSPLGF_(—)1_P4 (SEQ ID NO:99) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSPLGF_(—)1_T2 (SEQ IDNO:96). An alignment is given to the known protein (Placenta growthfactor precursor) at the end of the application. in the alignment tableon the attached CD-ROM. A brief description of the relationship of thevariant protein according to the present invention to each such alignedprotein is as follows:

1. Comparison Report Between HSPLGF_(—)1_P4 (SEQ ID NO:99) and P49763-2(SEQ ID NO: 536):

A. An isolated chimeric polypeptide as set forth in HSPLGF_(—)1_P4 (SEQID NO:99), comprising a first amino acid sequence being at least 90%homologous toMPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEEMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLREKMKPEcorresponding to amino acids 1-140 of P49763-2 (SEQ ID NO: 536), whichalso corresponds to amino acids 1-140 of HSPLGF_(—)1_P4 (SEQ ID NO:99),and a second amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceSHLVLTLGLLQEETQGQGEEEEREAETHRLPPVRRCCSPEVTHPLEERDPAPGSCIYYRHTLQ (SEQ IDNO: 480) corresponding to amino acids 141-203 of HSPLGF_(—)1_P4 (SEQ IDNO:99), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion ofHSPLGF_(—)1_P4 (SEQ ID NO:99), comprising an amino acid sequence beingat least 70%, optionally at least about 80%, preferably at least about85%, more preferably at least about 90% and most preferably at leastabout 95% homologous to the sequenceSHLVLTLGLLQEETQGQGEEEEREAETHRLPPVRRCCSPEVTHPLEERDPAPGSCIYYRHTLQ (SEQ IDNO: 480) of HSPLGF_(—)1_P4 (SEQ ID NO:99).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 121:

TABLE 121 InterPro domain(s) Position(s) Domain description Analysistype on protein Platelet-derived growth factor (PDGF) BlastProDom 43-129Platelet-derived growth factor (PDGF) HMMPfam 52-130 Platelet-derivedgrowth factor (PDGF) HMMSmart 50-132 Platelet-derived growth factor(PDGF) ProfileScan 39-135 Platelet-derived growth factor (PDGF)ScanRegExp 75-87 

Variant protein HSPLGF_(—)1_P4 (SEQ ID NO:99) is encoded by thefollowing transcript(s): HSPLGF_(—)1_T2 (SEQ ID NO:96), for which thecoding portion starts at position 523 and ends at position 1131. Thetranscript also has the following SNPs as listed in Table 122 (givenaccording to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein HSPLGF_(—)1_P4 (SEQ ID NO:99) sequence provides support for thededuced sequence of this variant protein according to the presentinvention).

TABLE 122 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> T  132 T -> C  166 G -> A 293, 387, 1192 G ->  456 A -> T1253 A -> G 1305, 1686 C -> 1422 C -> T 1422 T -> A 1432 A -> 1464, 1466C -> G 1684 C -> A 1708

Variant protein HSPLGF_(—)1_P5 (SEQ ID NO:100) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSPLGF_(—)1_T6 (SEQ IDNO:97)

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

Variant protein HSPLGF_(—)1_P5 (SEQ ID NO:100) is encoded by thefollowing transcript(s): HSPLGF_(—)1_T6 (SEQ ID NO:97), for which thecoding portion starts at position 2 and ends at position 331. Thetranscript also has the following SNPs as listed in Table 123 (givenaccording to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein HSPLGF_(—)1_P5 (SEQ ID NO: 100) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 123 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 1464 A -> T 1525 A -> G 1577, 1958 C -> 1694 C -> T 1694T -> A 1704 A -> 1736, 1738 C -> G 1956 C -> A 1980

Variant protein HSPLGF_(—)1_P13 (SEQ ID NO:101) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSPLGF_(—)1_T15 (SEQ IDNO:98). An alignment is given to the known protein (Placenta growthfactor precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between HSPLGF_(—)1_P13 (SEQ ID NO: 101) andP49763-2 (SEQ ID NO: 536):

A. An isolated chimeric polypeptide as set forth in HSPLGF_(—)1_P13 (SEQID NO:101), comprising a amino acid sequence being at least 90%homologous toMPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLREKMKPERcorresponding to amino acids 1-141 of P49763-2 (SEQ ID NO: 536), whichalso corresponds to amino acids 1-141 of HSPLGF_(—)1_P13 (SEQ IDNO:101).

3.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 124:

TABLE 124 InterPro domain(s) Position(s) Domain description Analysistype on protein Platelet-derived growth factor (PDGF) BlastProDom 43-129Platelet-derived growth factor (PDGF) HMMPfam 52-130 Platelet-derivedgrowth factor (PDGF) HMMSmart 50-132 Platelet-derived growth factor(PDGF) ProfileScan 39-135 Platelet-derived growth factor (PDGF)ScanRegExp 75-87 

Variant protein HSPLGF_(—)1_P13 (SEQ ID NO:101) is encoded by thefollowing transcript(s): HSPLGF_l_T15 (SEQ ID NO:98), for coding portionstarts at position 523 and ends at position 945. The transcript also hasthe following SNPs as listed in Table 125 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HSPLGF_(—)1_P13(SEQ ID NO:101) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 125 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> T  132 T -> C  166 G -> A 293, 387, 1264 G ->  456 A -> T1325 A -> G 1377, 1758 C -> 1494 C -> T 1494 T -> A 1504 A -> 1536, 1538C -> G 1756 C -> A 1780

Variant protein HSPLGF_(—)1_P14 (SEQ ID NO:102) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HSPLGF_(—)1_T6 (SEQ IDNO:97).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is membrane.

Variant protein HSPLGF_(—)1_P14 (SEQ ID NO:102) is encoded by thefollowing transcript(s): HSPLGF_(—)1_T6 (SEQ ID NO:97), for which thecoding portion starts at position 846 and ends at position 1154. Thetranscript also has the following SNPs as listed in Table 126 (givenaccording to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein HSPLGF_(—)1_P14 (SEQ ID NO:102) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 126 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 1464 A -> T 1525 A -> G 1577, 1958 C -> 1694 C -> T 1694T -> A 1704 A -> 1736, 1738 C -> G 1956 C -> A 1980

As noted above, cluster HSPLGF features 11 segment(s), which were listedin Table 117 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segments 7, 15, 16, and 21 according to the present invention is nowprovided.

Segment cluster HSPLGF_(—)1_N7 (SEQ ID NO:107) according to the presentinvention is supported by 74 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSPLGF_(—)1_T15 (SEQ ID NO:98), HSPLGF_(—)1_T2(SEQ ID NO:96) and HSPLGF_(—)1_T6 (SEQ ID NO:97). Table 127 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 127 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSPLGF_1_T15 (SEQ ID NO: 98) 641837 HSPLGF_1_T2 (SEQ ID NO: 96) 641 837 HSPLGF_1_T6 (SEQ ID NO: 97) 10071203

Segment cluster HSPLGF_(—)1_N21 (SEQ ID NO:113) according to the presentinvention is supported by 154 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSPLGF_(—)1_T15 (SEQ ID NO:98), HSPLGF_(—)1_T2(SEQ ID NO:96) and HSPLGF_(—)1_T6 (SEQ ID NO:97). Table 128 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 128 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSPLGF_1_T15 (SEQ ID NO: 98) 11112015 HSPLGF_1_T2 (SEQ ID NO: 96) 1039 1943 HSPLGF_1_T6 (SEQ ID NO: 97)1311 2215

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster HSPLGF_(—)1_N15 (SEQ ID NO:110) according to the presentinvention is supported by 1 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSPLGF_(—)1_T15 (SEQ ID NO:98). Table 129 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 129 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSPLGF_1_T15 (SEQ ID NO: 98) 9451016

Segment cluster HSPLGF_(—)1_N16 (SEQ ID NO:111) according to the presentinvention is supported by 2 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HSPLGF_l_T15 (SEQ ID NO:98) and HSPLGF_(—)1_T2(SEQ ID NO:96). Table 130 below describes the starting and endingposition of this segment on each transcript.

TABLE 130 Segment location on transcripts Segment Segment Transcriptname starting position ending position HSPLGF_1_T15 (SEQ ID NO: 98) 10171047 HSPLGF_1_T2 (SEQ ID NO: 96) 945 975

FIG. 15 shows the structure of the HSPLGF mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe. Expression of Homo sapiens placental growth factor, vascularendothelial growth factor-related protein (PlGF) HSPLGF transcriptswhich are detectable by amplicon as depicted in sequence nameHSPLGF_seg7WT (SEQ ID NO:393) in normal and cancerous Lung tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by oraccording to seg7_WT—HSPLGF_seg7_WT (SEQ ID NO:393) amplicon and primersHSPLGF_seg7F_WT (SEQ ID NO:394) and HSPLGF_seg7R_WT (SEQ ID NO:395) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes —HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ IDNO: 379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBankAccession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ IDNO:382)), SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)) and Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)) was measured similarly. For each RT sample, the expression ofthe above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (sample numbers 47, 48, 49, 50, 90, 91, 92, 93,96, 97, 98 and 99, Table 3 above), to obtain a value of foldup-regulation for each sample relative to median of the normal PMsamples.

FIG. 16 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PLGF) transcripts in cancerous Lung samplesrelative to the normal samples.

As is evident from FIG. 16, the expression of Homo sapiens placentalgrowth factor, vascular endothelial growth factor-related protein (PlGF)transcripts detectable by the above amplicon in small cell carcinomasamples was significantly higher than in the non-cancerous samples(sample numbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table3 above) and was higher in a few non-small cell carcinoma samples thanin the non-cancerous samples. Notably an over-expression of at least 5fold was found in 4 out of 8 small cell carcinoma samples and in 4 outof 35 non-small cell carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapiensplacental growth factor, vascular endothelial growth factor-relatedprotein (PlGF) transcripts detectable by the above amplicon in Lungadenocarcinoma samples versus the normal tissue samples was determinedby T test as 3.85e-002. The P value for the difference in the expressionlevels of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by the aboveamplicon in Lung small cell carcinoma samples versus the normal tissuesamples was determined by T test as 1.30e-002. The P value for thedifference in the expression levels of Homo sapiens placental growthfactor, vascular endothelial growth factor-related protein (PlGF)transcripts detectable by the above amplicon in Lung non-small cellcarcinoma samples versus the normal tissue samples was determined by Ttest as 7.42e-003.

Threshold of 5 fold over expression was found to differentiate betweensmall cell carcinoma and normal samples with P value of 1.44e-002 aschecked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSPLGF_seg7F_WT (SEQ ID NO:394) forward primer;and HSPLGF_seg7R_WT (SEQ ID NO:395) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSPLGF_seg7_WT (SEQ IDNO:393).

Forward Primer (HSPLGF_seg7F_WT (SEQ ID NO:394)): TCGTGTCCGAGTACCCCAGReverse Primer (HSPLGF_seg7R_WT (SEQ ID NO:395)): ACAGTGCAGATTCTCATCGCCAmplicon (HSPLGF_seg7_WT (SEQ ID NO:393)):TCGTGTCCGAGTACCCCAGCGAGGTGGAGCACATGTTCAGCCCATCCTGTGTCTCCCTGCTGCGCTGCACCGGCTGCTGCGGCGATGAGAATCTGCACTG TExpression of Homo sapiens Placental Growth Factor, Vascular EndothelialGrowth Factor-Related Protein (PGF) HSPLGF Transcripts which areDetectable by Amplicon as Depicted in Sequence Name HSPLGF_seg7WT (SEQID NO: 393) in Different Normal Tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PGF) transcripts detectable by oraccording to seg7WT—HSPLGF_seg7WT (SEQ ID NO: 393) amplicon and primersHSPLGF_seg7WTF (SEQ ID NO: 394) and HSPLGF_seg7WTR (SEQ ID NO: 395) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the placenta samples (samplenumbers 30, 31 and 32, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the placenta samples.FIG. 17 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg7WT (SEQ ID NO: 393) in different normal tissues.

Forward Primer (HSPLGF_seg7WTF (SEQ ID NO: 394)): TCGTGTCCGAGTACCCCAGReverse Primer (HSPLGF_seg7WTR (SEQ ID NO: 395)): ACAGTGCAGATTCTCATCGCCAmplicon (HSPLGF_seg7WT (SEQ ID NO: 393)):TCGTGTCCGAGTACCCCAGCGAGGTGGAGCACATGTTCAGCCCATCCTGTGTCTCCCTGCTGCGCTGCACCGGCTGCTGCGGCGATGAGAATCTGCACTG T

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) HSPLGF transcripts which aredetectable by amplicon as depicted in sequence name HSPLGF_seg15-16 (SEQID NO:396) in different normal tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by oraccording to seg15-16—HSPLGF_seg15-16 (SEQ ID NO:396) amplicon andprimers HSPLGF_seg15-16F (SEQ ID NO:397) and HSPLGF_seg15-16R (SEQ IDNO:398) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the placenta samples (samplenumbers 30, 31 and 32, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the placenta samples.FIG. 18 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PlGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg15-16 (SEQ ID NO:396) in different normal tissues.

Forward Primer (HSPLGF_seg15-16F (SEQ ID NO:397)): TGGTTTGGCTGGGGCTCReverse Primer (HSPLGF_seg15-16R (SEQ ID NO:398)): CTGCAATAAGCCAAGCGTCAGAmplicon (HSPLGF_seg15-16 (SEQ ID NO:396)):TGGTTTGGCTGGGGCTCGGGGCTATTCTCGGGCCTGCCAGCCTCTGTCCTAGCATGGGGTTCCCCAGCCACCTTGTCCTGACGCTTGGCTTATTGCAGExpression of Homo sapiens Placental Growth Factor, Vascular EndothelialGrowth Factor-Related Protein (PlGF) HSPLGF Transcripts which areDetectable by Amplicon as Depicted in Sequence Name HSPLGF_seg16-21 (SEQID NO:399) in Normal and Cancerous Lung Tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by oraccording to seg16-21—HSPLGF_seg16-21 (SEQ ID NO:399) amplicon andprimers HSPLGF_seg16-21F (SEQ ID NO:400) and HSPLGF_seg16-21R (SEQ IDNO:401) was measured by real time PCR. In parallel the expression offour housekeeping genes —HPRT1 (GenBank Accession No. NM_(—)000194 (SEQID NO: 379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBankAccession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ IDNO:382)), SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)) and Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)) was measured similarly. For each RT sample, the expression ofthe above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (sample numbers 47, 48, 49, 50, 90, 91, 92, 93,96, 97, 98 and 99, Table 3 above), to obtain a value of foldup-regulation for each sample relative to median of the normal PMsamples.

FIG. 19 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) transcripts in cancerous Lung samplesrelative to the normal samples (seg16-21).

As is evident from FIG. 19, the expression of Homo sapiens placentalgrowth factor, vascular endothelial growth factor-related protein (PlGF)transcripts detectable by the above amplicon in adenocarcinoma and smallcell carcinoma samples was higher than in the non-cancerous samples(sample numbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table3 above) and was higher in a few squamous cell carcinoma. Notably anover-expression of at least 5 fold was found in 5 out of 15adenocarcinoma samples, in 3 out of 16 squamous cell carcinoma samples,in 5 out of 8 small cell carcinoma.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapiensplacental growth factor, vascular endothelial growth factor-relatedprotein (PlGF) transcripts detectable by the above amplicon in Lungadenocarcinoma samples versus the normal tissue samples was determinedby T test as 2.90e-002. The P value for the difference in the expressionlevels of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by the aboveamplicon in Lung squamous cell carcinoma samples versus the normaltissue samples was determined by T test as 1.67e-002. The P value forthe difference in the expression levels of Homo sapiens placental growthfactor, vascular endothelial growth factor-related protein (PGF)transcripts detectable by the above amplicon in all Lung non-small cellcarcinoma samples versus the normal tissue samples was determined by Ttest as 6.04e-003. The P value for the difference in the expressionlevels of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by the aboveamplicon in Lung small cell carcinoma samples versus the normal tissuesamples was determined by T test as 1.11e-002.

Threshold of 5 fold over expression was found to differentiate betweenadenocarcinoma and normal samples with P value of 3.72e-002 as checkedby exact Fisher test. Threshold of 5 fold over expression was found todifferentiate between small cell carcinoma and normal samples with Pvalue of 3.61e-003 as checked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSPLGF_seg16-21F (SEQ ID NO:400) forward primer;and HSPLGF_seg16-21R (SEQ ID NO:401) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSPLGF_seg16-21 (SEQID NO:399).

Forward Primer (HSPLGF_seg16-21F (SEQ ID NO:400)): CTTGTCCTGACGCTTGGCTTAReverse Primer (HSPLGF_seg16-21R (SEQ ID NO:401)): GGGAACAGCATCGCCGAmplicon HSPLGF_seg16-21 (SEQ ID NO:399)CTTGTCCTGACGCTTGGCTTATTGCAGGAGGAGACCCAAGGGCAGGGGGAAGAGGAGGAGAGAGAAGCAGAGACCCACAGACTGCCACCTGTGCGGCGAT GCTGTTCCCExpression of Homo sapiens Placental Growth Factor, Vascular EndothelialGrowth Factor-Related Protein (PlGF) HSPLGF Transcripts which areDetectable by Amplicon as Depicted in Sequence Name HSPLGF_seg16-21 (SEQID NO:399) in Normal and Cancerous Colon Tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by oraccording to seg16-21—HSPLGF_seg16-21 (SEQ ID NO:399) amplicon andprimers HSPLGF_seg16-21F (SEQ ID NO:400) and HSPLGF_seg16-21R (SEQ IDNO:401) was measured by real time PCR. In parallel the expression offour housekeeping genes—HPRT1 (GenBank Accession No. NM_(—)000194 (SEQID NO: 379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBankAccession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ IDNO:382)), RPS27A (GenBank Accession No. NM_(—)002954 (SEQ ID NO:403);RPS27A (SEQ ID NO:402) amplicon) and G6PD (GenBank Accession No.NM_(—)000402 (SEQ ID NO:405); G6PD (SEQ ID NO:404) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the normal post-mortem (PM)samples (sample numbers 41, 52, 63, 64, 65, 66, 67, 69, 70 and 71, Table2 above), to obtain a value of fold up-regulation for each samplerelative to median of the normal PM samples.

FIG. 20 is a histogram showing over expression of the above-indicatedHomo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) transcripts in cancerous Colon samplesrelative to the normal samples (seg16-21).

As is evident from FIG. 20, the expression of Homo sapiens placentalgrowth factor, vascular endothelial growth factor-related protein (PGF)transcripts detectable by the above amplicon in cancer samples washigher than in the non-cancerous samples (sample numbers 41, 52, 63, 64,65, 66, 67, 69, 70 and 71, Table 2 above). Notably an over-expression ofat least 5 fold was found in 7 out of 33 adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapiensplacental growth factor, vascular endothelial growth factor-relatedprotein (PlGF) transcripts detectable by the above amplicon in Coloncancer samples versus the normal tissue samples was determined by T testas 9.07e-003.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HSPLGF_seg16-21F (SEQ ID NO:400) forward primer;and HSPLGF_seg16-21R (SEQ ID NO:401) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HSPLGF_seg16-21 (SEQID NO:399).

Forward Primer (HSPLGF_seg16-21F (SEQ ID NO:400)): CTTGTCCTGACGCTTGGCTTAReverse Primer (HSPLGF_seg16-21R (SEQ ID NO:401)): GGGAACAGCATCGCCGAmplicon (HSPLGF_seg16-21 (SEQ ID NO:399))CTTGTCCTGACGCTTGGCTTATTGCAGGAGGAGACCCAAGGGCAGGGGGAAGAGGAGGAGAGAGAAGCAGAGACCCACAGACTGCCACCTGTGCGGCGAT GCTGTTCCCExpression of Homo sapiens Placental Growth Factor, Vascular EndothelialGrowth Factor-Related Protein (PlGF) HSPLGF Transcripts which areDetectable by Amplicon as Depicted in Sequence Name HSPLGF_seg16-21 (SEQID NO:399) in Different Normal Tissues

Expression of Homo sapiens placental growth factor, vascular endothelialgrowth factor-related protein (PlGF) transcripts detectable by oraccording to seg16-21—HSPLGF_seg16-21 (SEQ ID NO:399) amplicon andprimers HSPLGF_seg16-21F (SEQ ID NO:400) and HSPLGF_seg16-21R (SEQ IDNO:401) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the placenta samples (samplenumbers 30, 31 and 32, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the placenta samples.FIG. 21 shows expression of Homo sapiens placental growth factor,vascular endothelial growth factor-related protein (PlGF) HSPLGFtranscripts which are detectable by amplicon as depicted in sequencename HSPLGF_seg16-21 (SEQ ID NO:399) in different normal tissues.

Forward Primer (HSPLGF_seg16-21F (SEQ ID NO:400)): CTTGTCCTGACGCTTGGCTTAReverse Primer (HSPLGF_seg16-21R (SEQ ID NO:401)): GGGAACAGCATCGCCGAmplicon (HSPLGF_seg16-21 (SEQ ID NO:399))CTTGTCCTGACGCTTGGCTTATTGCAGGAGGAGACCCAAGGGCAGGGGGAAGAGGAGGAGAGAGAAGCAGAGACCCACAGACTGCCACCTGTGCGGCGAT GCTGTTCCC

Homo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) HSPLGF transcripts which are detectable byamplicon as depicted in sequence name HSPLGF_seg7WT (SEQ ID NO: 393) andprimers HSPLGF_seg7WT-F (SEQ ID NO: 394) and HSPLGF_seg7WT-R (SEQ ID NO:395) did not show any differential expression in one experiment carriedout with each of the following cancer panels: breast cancer, coloncancer and ovary cancer.

Homo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) HSPLGF transcripts which are detectable byamplicon as depicted in sequence name HSPLGF_seg15-16 (SEQ ID NO:396)and primers HSPLGF_seg15-16-F (SEQ ID NO: 397) and HSPLGF_seg15-16-R(SEQ ID NO: 398) did not show any differential expression in oneexperiment carried out with colon cancer panel.

Homo sapiens placental growth factor, vascular endothelial growthfactor-related protein (PGF) HSPLGF transcripts which are detectable byamplicon as depicted in sequence name HSPLGF_seg16-21 (SEQ ID NO:399)and primers HSPLGF_seg16-21-F (SEQ ID NO: 400) and HSPLGF_seg16-21-R(SEQ ID NO: 401) did not show any differential expression in oneexperiment carried out with each of the following cancer panels: breastcancer and ovary cancer.

Description for Cluster HUMSP18A

Cluster HUMSP18A features 13 transcript(s) and 50 segment(s) ofinterest, the names for which are given in Tables 131 and 132,respectively. The selected protein variants are given in table 133.

TABLE 131 Transcripts of interest Transcript Name HUMSP18A_T14 (SEQ IDNO: 114) HUMSP18A_T15 (SEQ ID NO: 115) HUMSP18A_T20 (SEQ ID NO: 116)HUMSP18A_T23 (SEQ ID NO: 117) HUMSP18A_T27 (SEQ ID NO: 118) HUMSP18A_T29(SEQ ID NO: 119) HUMSP18A_T30 (SEQ ID NO: 120) HUMSP18A_T34 (SEQ ID NO:121) HUMSP18A_T35 (SEQ ID NO: 122) HUMSP18A_T38 (SEQ ID NO: 123)HUMSP18A_T42 (SEQ ID NO: 124) HUMSP18A_T44 (SEQ ID NO: 125) HUMSP18A_T46(SEQ ID NO: 126)

TABLE 132 Segments of interest Segment Name HUMSP18A_N2 (SEQ ID NO: 140)HUMSP18A_N9 (SEQ ID NO: 143) HUMSP18A_N15 (SEQ ID NO: 148) HUMSP18A_N17(SEQ ID NO: 150) HUMSP18A_N26 (SEQ ID NO: 158) HUMSP18A_N28 (SEQ ID NO:160) HUMSP18A_N29 (SEQ ID NO: 161) HUMSP18A_N31 (SEQ ID NO: 163)HUMSP18A_N32 (SEQ ID NO: 164) HUMSP18A_N44 (SEQ ID NO: 172) HUMSP18A_N67(SEQ ID NO: 183) HUMSP18A_N68 (SEQ ID NO: 184) HUMSP18A_N69 (SEQ ID NO:185) HUMSP18A_N70 (SEQ ID NO: 186) HUMSP18A_N72 (SEQ ID NO: 188)HUMSP18A_N0 (SEQ ID NO: 139) HUMSP18A_N5 (SEQ ID NO: 141) HUMSP18A_N6(SEQ ID NO: 142) HUMSP18A_N10 (SEQ ID NO: 144) HUMSP18A_N11 (SEQ ID NO:145) HUMSP18A_N13 (SEQ ID NO: 146) HUMSP18A_N14 (SEQ ID NO: 147)HUMSP18A_N16 (SEQ ID NO: 149) HUMSP18A_N18 (SEQ ID NO: 151) HUMSP18A_N19(SEQ ID NO: 152) HUMSP18A_N20 (SEQ ID NO: 153) HUMSP18A_N21 (SEQ ID NO:154) HUMSP18A_N22 (SEQ ID NO: 155) HUMSP18A_N23 (SEQ ID NO: 156)HUMSP18A_N25 (SEQ ID NO: 157) HUMSP18A_N27 (SEQ ID NO: 159) HUMSP18A_N30(SEQ ID NO: 162) HUMSP18A_N33 (SEQ ID NO: 165) HUMSP18A_N34 (SEQ ID NO:166) HUMSP18A_N35 (SEQ ID NO: 167) HUMSP18A_N36 (SEQ ID NO: 168)HUMSP18A_N37 (SEQ ID NO: 169) HUMSP18A_N38 (SEQ ID NO: 170) HUMSP18A_N39(SEQ ID NO: 171) HUMSP18A_N45 (SEQ ID NO: 173) HUMSP18A_N46 (SEQ ID NO:174) HUMSP18A_N50 (SEQ ID NO: 175) HUMSP18A_N51 (SEQ ID NO: 176)HUMSP18A_N52 (SEQ ID NO: 177) HUMSP18A_N62 (SEQ ID NO: 178) HUMSP18A_N63(SEQ ID NO: 179) HUMSP18A_N64 (SEQ ID NO: 180) HUMSP18A_N65 (SEQ ID NO:181) HUMSP18A_N66 (SEQ ID NO: 182) HUMSP18A_N71 (SEQ ID NO: 187)

TABLE 133 Proteins of interest Protein Name Corresponding Transcript(s)HUMSP18A_P3 (SEQ ID NO: 127) HUMSP18A_T14 (SEQ ID NO: 114); HUMSP18A_T30(SEQ ID NO: 120) HUMSP18A_P20 (SEQ ID NO: 128) HUMSP18A_T44 (SEQ ID NO:125) HUMSP18A_P22 (SEQ ID NO: 129) HUMSP18A_T46 (SEQ ID NO: 126)HUMSP18A_P38 (SEQ ID NO: 130) HUMSP18A_T14 (SEQ ID NO: 114);HUMSP18A_T30 (SEQ ID NO: 120) HUMSP18A_P39 (SEQ ID NO: 131) HUMSP18A_T15(SEQ ID NO: 115); HUMSP18A_T27 (SEQ ID NO: 118) HUMSP18A_P41 (SEQ ID NO:132) HUMSP18A_T20 (SEQ ID NO: 116) HUMSP18A_P43 (SEQ ID NO: 133)HUMSP18A_T23 (SEQ ID NO: 117) HUMSP18A_P45 (SEQ ID NO: 134) HUMSP18A_T29(SEQ ID NO: 119) HUMSP18A_P48 (SEQ ID NO: 135) HUMSP18A_T34 (SEQ ID NO:121) HUMSP18A_P49 (SEQ ID NO: 136) HUMSP18A_T35 (SEQ ID NO: 122)HUMSP18A_P50 (SEQ ID NO: 137) HUMSP18A_T38 (SEQ ID NO: 123) HUMSP18A_P53(SEQ ID NO: 138) HUMSP18A_T42 (SEQ ID NO: 124)

These sequences are variants of the known protein Pulmonarysurfactant-associated protein B precursor (SwissProt accessionidentifier PSPB_HUMAN (SEQ ID NO:406); known also according to thesynonyms SP-B; 6 kDa protein; Pulmonary surfactant-associatedproteolipid SPL(Phe); 18 kDa pulmonary-surfactant protein), referred toherein as the previously known protein.

Protein Pulmonary surfactant-associated protein B precursor is known orbelieved to have the following function(s): Pulmonarysurfactant-associated proteins promote alveolar stability by loweringthe surface tension at the air-liquid interface in the peripheral airspaces. SP-B increases the collapse pressure of palmitic acid to nearly70 millinewtons per meter. Known polymorphisms for this sequence are asshown in Table 134.

TABLE 134 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 131 T -> I (in dbSNP: 1130866). /FTId =VAR_006948 176 L -> F (in dbSNP: 3024801). /FTId = VAR_013099 228 A ->R. /FTId = VAR_006949 228 A -> I. /FTId = VAR_006950 272 R -> H (indbSNP: 3024809). /FTId = VAR_013100 178 L -> V 318 P -> L

Protein Pulmonary surfactant-associated protein B precursor localizationis believed to be extracellular.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: organogenesis; respiratorygaseous exchange, which are annotation(s) related to Biological Process.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

According to optional embodiments of the present invention, variants ofthis cluster according to the present invention (amino acid and/ornucleic acid sequences of HUMSP18A) may optionally have one or more ofthe following utilities, as described with regard to the Table below. Itshould be noted that these utilities are optionally and preferablysuitable for human and non-human animals as subjects, except whereotherwise noted. The reasoning is described with regard to biologicaland/or physiological and/or other information about the known protein,but is given to demonstrate particular diagnostic utility for thevariants according to the present invention.

Pulmonary surfactant-associated protein B play an important role in thestability and spreading of surfactant lipids in the alveolus. Deletionor mutations in SP-B cause acute and chronic lung disease (Biol Neonate.2005; 87(4):283-7. Epub 2005 Jun. 1). Also see below:

TABLE 135 Utilities for Variants of HUMSP18A, related to Pulmonarysurfactant-associated protein B Dx field Explanation Ref A marker forLung Partial SP-B deficiency perturbs Am J Physiol Lung Cell Molfunction/damage/respiratory lung function and causes Physiol. 2005 Jun;288(6): L1154-61. failure respiratory failure Epub 2005 Feb 18 Crit CareMed. 2004 May; 32(5): 1115-9 J Perinat Neonatal Nurs. 2004 Jan-Mar;18(1): 61-7. Surrogate marker for lung Dexamethasone and Am J ObstetGynecol. 2004 adenocarcinoma treatment betamethasone affect surfactantApr; 190(4): 952-9 protein-B messenger RNA expression in human type IIpneumocytes and human lung adenocarcinoma cells A biomarker in chronicheart Plasma SP-B was elevated in Circulation. 2004 Aug failure CHF (P <0.001), and levels 31; 110(9): 1091-6. Epub 2004 A surrogate marker forthe effect increased with New York Heart Aug 9 of diuretics on CHFAssociation classification (P < 0.001). SP-B levels are correlated withclinical severity. During follow-up, major cardiovascular eventsoccurred in patients with higher plasma SP-B (P < 0.01) and NT-proBNP (P< 0.05). Furthermore, on conditional logistic regression analysis, onlySP-B was independently associated with CHF hospitalization (P = 0.005).Therefore, it may be a clinically useful biomarker of the pulmonaryconsequences of raised P(mv). When the diuretic dosage was increased onclinical grounds, SP- B had increased 39% (P < 0.001)

According to other optional embodiments of the present invention,variants of this cluster according to the present invention (amino acidand/or nucleic acid sequences of HUMSP18A) may optionally have one ormore of the following utilities, some of which are related to utilitiesdescribed above. It should be noted that these utilities are optionallyand preferably suitable for human and non-human animals as subjects,except where otherwise noted.

A non-limiting example of such a utility is using this marker as asurrogate marker for determining the efficacy of treatment for variouslung and cardiovascular disorders, including but not limited to thefollowing: lung cancer, lung function failure. The surrogate markeraccording to the present invention could be measured in subjectsundergoing treatment including but not limited to the following:treatment of lung cancer by surgery, radiation and/or chemotherapy. Themost commonly used chemotherapeutic agents for the treatment of lungcancer include but are not limited to Platinol® (Generic Name:Cisplatin), VP-16; VePesid® (Generic Name: Etoposide), Paraplatin®(Generic Name: Carboplatin), Taxol® (Generic Name: Paclitaxel),Taxotere® (Generic Name: Docetaxel), Navelbine® (Generic Name:Vinorelbine tartrate), Adriamycin® (Generic Name: Doxorubicin), Oncovin®(Generic Name: Vincristine sulfate), Ifex® (Generic Name: Ifosfamide),Gemzar® (Generic Name: Gemcitabine hydrochloride). Standard chemotherapyfor lung cancer typically consists of combinations of two or more ofthese drugs. Such combination therapy has been shown to improve theoverall response to treatment. Well-known drug pairings in combinationtherapy include: paclitaxel plus carboplatin; cisplatin plus vinorelbinetartrate; cisplatin plus VP-16; and carboplatin plus VP-16. Concurrentradiotherapy is very often used with the combinations of cisplatin plusVP-16 or carboplatin plus VP-16. Other chemotherapeutic agents that maybe used to treat lung cancer during clinical trials or alternativeprograms are: Cytoxan® (Generic Name: Cyclophosphamide); Methotrexate(Generic Name: Methotrexate); CeeNu® (Generic Name: Lomustine (CCNU))and Hycamtimm (Generic Name: Topotecan.hydrochloride).

The surrogate marker according to the present invention could bemeasured in subjects undergoing treatment including but not limited tothe following: treatments of lung function failure using respirationwith oxygen (plus PEEP pressure), steroids, surfactant, inhaled nitricoxide.

Another non-limiting example of diagnostic utility of one or moreHSACMHCP variants according to the present invention may optionally bedetection of Lung Adenocarcinoma, as described for example inBhattacharjee A, et al (Proc Natl Acad Sci USA. 2001 Nov. 20;98(24):13790-5) through microarrays.

Other non-limiting exemplary utilities for HUMSP18A variants accordingto the present invention are described in greater detail below and alsowith regard to the previous section on clinical utility.

As noted above, cluster HUMSP18A features 13 transcript(s), which werelisted in Table 131 above. These transcript(s) encode for protein(s)which are variant(s) of protein Pulmonary surfactant-associated proteinB precursor. A description of each variant protein according to thepresent invention is now provided.

Variant protein HUMSP18A_P3 (SEQ ID NO:127) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T14 (SEQ ID NO:114)and HUMSP18A_T30 (SEQ ID NO:120). An alignment is given to the knownprotein (Pulmonary surfactant-associated protein B precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMSP18A_P3 (SEQ ID NO:127) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P3 (SEQ IDNO:127), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MHQAGYPGCRGA (SEQ ID NO: 582) corresponding to aminoacids 1-12 of HUMSP18A_P3 (SEQ ID NO:127), a second amino acid sequencebeing at least 90% homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPcorresponding to amino acids 1-285 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 13-297 of HUMSP18A_P3 (SEQ ID NO:127),and a third amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceSEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) corresponding to amino acids298-319 of HUMSP18A_P3 (SEQ ID NO:127), wherein said first amino acidsequence, second amino acid sequence and third amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMSP18A_P3 (SEQ IDNO:127), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MHQAGYPGCRGA (SEQ ID NO: 582) of HUMSP18A_P3 (SEQ ID NO:127).

C. An isolated polypeptide encoding for an edge portion of HUMSP18A_P3(SEQ ID NO:127), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence SEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) ofHUMSP18A_P3 (SEQ ID NO:127).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P3 (SEQ ID NO:127) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table136, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P3 (SEQ ID NO:127) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 136 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 2 H -> P 16 S -> 27 P -> L 46 Q -> 72 W -> *110 Q -> R 131 Y -> F 134 L -> 143 T -> I 172 L -> 172 L -> Q 178 D ->188 L -> F 196 A -> 201 P -> 211 Q -> L 220 C -> Y 227 I -> N 234 I -> V240 A -> G 240 A -> P 255 G -> 255 G -> D 275 G -> 276 R -> 284 R -> H292 D -> G 303 P -> H 309 L -> P

The glycosylation sites of variant protein HUMSP18A_P3 (SEQ ID NO:127),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 137 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 137 Glycosylation site(s) Position(s) on known amino acid Presentin variant Position(s) on sequence protein? variant protein 141 Yes 153311 No

Variant protein HUMSP18A_P3 (SEQ ID NO:127) is encoded by the followingtranscript(s): HUMSP18A_T14 (SEQ ID NO:114) and HUMSP18A_T30 (SEQ IDNO:120), for which the coding portion starts at position 101 and ends atposition 1057. The transcript also has the following SNPs as listed inTable 138 (given according to their position on the nucleotide sequence,with the alternative nucleic acid listed; the presence of known SNPs invariant protein HUMSP18A_P3 (SEQ ID NO:127) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 138 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1176, 3115, 3225, 3302A -> C 105, 2622 T -> 146 C -> T 180, 208, 466, 528, 662, 979, 1937,2046, 2311, 3189, 3246 G -> 238, 864, 924, 1248, 2207 A -> G 429, 800,1021, 975, 1689, 1925, 2266, 3232, 3244 A -> T 492, 732, 1957 C -> 500,687, 701, 614, 634, 928, 1353, 2440 T -> A 615, 780 G -> C 818, 2115 C-> G 819, 1612, 2210, 3333 T -> G 820, 3199, 3236 T -> C 820, 3205, 1026C -> A 1008, 3333 G -> T 1600, 3325 C -> T 1805 A -> 1955

The coding portion of transcript HUMSP18A_T30 (SEQ ID NO:120) starts atposition 101 and ends at position 1057. The transcript also has thefollowing SNPs as listed in Table 139 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HUMSP18A_P3 (SEQ IDNO:127) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 139 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1176, 1324, 3285,3395, 3472 A -> C 105, 2792 T -> 146 C -> T 180, 208, 466, 528, 662,979, 1975, 2107, 2216, 2481, 3359, 3416 G -> 238, 864, 924, 1248, 2377 A-> G 429, 800, 975, 1021, 1859, 2095, 2436, 3402, 3414 A -> T 492, 732,2127 C -> 500, 614, 634, 687, 701, 928, 1523, 2610 T -> A 615, 780 G ->C 818, 2285 C -> G 819, 1782, 2380, 3503 T -> G 820, 3369, 3406 T -> C820, 1026, 3375 C -> A 1008, 3503 G -> T 1770, 3495 A -> 2125

Variant protein HUMSP18A_P20 (SEQ ID NO:128) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T44 (SEQ IDNO:125). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P20 (SEQ ID NO:128) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P20 (SEQ IDNO:128), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ(SEQ ID NO: 583) corresponding to amino acids 1-49 of HUMSP18A_P20 (SEQID NO:128), and a second amino acid sequence being at least 90%homologous to DDLCQECEDILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREKCKQFVEQHTPQLLTLVPRGWDAHTTCQALGVCGTMSSPLQCIHSPDL corresponding to amino acids 66-381 of PSPB_HUMAN(SEQ ID NO:406), which also corresponds to amino acids 50-365 ofHUMSP18A_P20 (SEQ ID NO:128), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMSP18A_P20 (SEQ IDNO: 128), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO:583) of HUMSP18A_P20 (SEQ ID NO:128).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P20 (SEQ ID NO:128) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table140, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P20 (SEQ ID NO:128) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 140 Amino acid mutations SNP position(s) on amino acid Alternativesequence amino acid(s) 47 P -> H 82 Q -> R 103 Y -> F 106 L -> 115 T ->I 144 L -> 144 L -> Q 150 D -> 160 L -> F 168 A -> 173 P -> 183 Q -> L192 C -> Y 199 I -> N 206 I -> V 212 A -> G 212 A -> P 227 G -> 227 G ->D 247 G -> 248 R -> 256 R -> H 264 D -> G 274 G -> R 298 E -> 333 L ->

The glycosylation sites of variant protein HUMSP18A_P20 (SEQ ID NO:128),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 141 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 141 Glycosylation site(s) Position(s) on known amino Present inPosition(s) on acid sequence variant protein? variant protein 178 Yes162 360 Yes 344

Variant protein HUMSP18A_P20 (SEQ ID NO:128) is encoded by the followingtranscript(s): HUMSP18A_T44 (SEQ ID NO:125), for which the codingportion starts at position 108 and ends at position 1202. The transcriptalso has the following SNPs as listed in Table 142 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP118A_P20(SEQ ID NO:128) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 142 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> A 247, 3084 G -> A 350, 682, 787, 874, 927, 2866, 2976,3053 A -> G 352, 723, 898, 1440, 1676, 2017, 2983, 2995 C -> T 389, 451,585, 902, 1556, 1688, 1797, 2062, 2940, 2997 A -> T 415, 655, 1708 C ->423, 537, 610, 624, 851, 557, 1104, 2191 T -> A 538, 703 G -> C 741,1866 C -> G 742, 1363, 1961, 3084 T -> G 743, 2950, 2987 T -> C 743,2956 G -> 787, 847, 999, 1958 G -> T 1351, 3076 A -> 1706 A -> C 2373

Variant protein HUMSP18A_P22 (SEQ ID NO:129) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T46 (SEQ IDNO:126). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P22 (SEQ ID NO:129) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P22 (SEQ IDNO:129), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ(SEQ ID NO: 583) corresponding to amino acids 1-49 of HUMSP18A_P22 (SEQID NO:129), a second amino acid sequence being at least 90% homologousto DDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTcorresponding to amino acids 66-131 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 50-115 of HUMSP18A_P22 (SEQ ID NO:129),and a third amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHKHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHMTTQHPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHTHSTPAGHTHTHTHPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLTHMLTBLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) corresponding to amino acids 116-344 ofHUMSP18A_P22 (SEQ ID NO:129), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

B. An isolated polypeptide encoding for a head of HUMSP18A_P22 (SEQ IDNO:129), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MDEMGQVGLVGSCMCLGVLCWPLPKRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO:583) of HUMSP18A_P22 (SEQ ID NO:129).

C. An isolated polypeptide encoding for an edge portion of HUMSP18A_P22(SEQ ID NO:129), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHKHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHTHTQHPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHTHSTPAGHTHTHTHPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLTHMLTHLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) of HUMSP18A_P22 (SEQ ID NO:129).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P22 (SEQ ID NO:129) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table143, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P22 (SEQ ID NO:129) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 143 Amino acid mutations SNP position(s) on amino acid Alternativesequence amino acid(s) 47 P -> H 82 Q -> R 103 Y -> F 106 L -> 115 T ->I 249 Q -> E

The glycosylation sites of variant protein HUMSP18A_P22 (SEQ ID NO:129),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 144 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 144 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 178Yes 162 311 No

Variant protein HUMSP18A_P22 (SEQ ID NO:129) is encoded by the followingtranscript(s): HUMSP18A_T46 (SEQ ID NO:126), for which the codingportion starts at position 108 and ends at position 1139. The transcriptalso has the following SNPs as listed in Table 145 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P22(SEQ ID NO:129) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 145 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence C -> A 247, 3906 G -> A 350, 1504, 1609, 1696 A -> G 352, 545,1545, 1720, 2262, 2498, 2839, 3805, 3817, C -> T 389, 451, 1407, 1724,2378, 2510, 2619, 2884, 3762, 3819 A -> T 415, 1477, 2530 C -> 423,1359, 1379, 1432, 1446, 1673, 1926, 3013 C -> G 852, 1564, 2185, 2783,3906 T -> A 1360, 1525, G -> C 1563, 2688 T -> G 1565, 3772, 3809 T -> C1565, 3778 G -> 1609, 1669, 1821, 2780 G -> A 1749, 3688, 3798, 3875, G-> T 2173, 3898 A -> 2528 A -> C 3195

Variant protein HUMSP18A_P38 (SEQ ID NO:130) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T14 (SEQ ID NO:114)and HUMSP18A_T30 (SEQ ID NO:120). An alignment is given to the knownprotein (Pulmonary surfactant-associated protein B precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMSP18A_P38 (SEQ ID NO:130) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P38 (SEQ IDNO:130), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPcorresponding to amino acids 1-285 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 1-285 of HUMSP18A_P38 (SEQ ID NO:130),and a second amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceSEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) corresponding to amino acids286-307 of HUMSP18A_P38 (SEQ ID NO:130), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P38(SEQ ID NO:130), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence SEPTAPSLAQCLLSSSPYPATA (SEQ ID NO: 481) ofHUMSP18A_P38 (SEQ ID NO:130).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P38 (SEQ ID NO:130) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table146, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P38 (SEQ ID NO:130) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 146 Amino acid mutations SNP position(s) on amino acid Alternativesequence amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R 119Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F 184 A-> 189 P -> 199 Q -> L 208 C -> Y 215 I -> N 222 I -> V 228 A -> G 228 A-> P 243 G -> 243 G -> D 263 G -> 264 R -> 272 R -> H 280 D -> G 291 P-> H 297 L -> P

The glycosylation sites of variant protein HUMSP18A_P38 (SEQ ID NO:130),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 147 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 147 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 129Yes 129 311 No

Variant protein HUMSP18A_P38 (SEQ ID NO:130) is encoded by the followingtranscript(s): HUMSP18A_T14 (SEQ ID NO:114) and HUMSP18A_T30 (SEQ IDNO:120), coding portion starts at position 137 and ends at position1057. The transcript also has the following SNPs as listed in Table 148(given according to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein HUMSP18A_P38 (SEQ ID NO:130) sequence provides support for thededuced sequence of this variant protein according to the presentinvention).

TABLE 148 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1176, 3115, 3225, 3302A -> C 105, 2622 T -> 146 C -> T 180, 208, 466, 528, 662, 979, 1805,1937, 2046, 2311, 3189, 3246 G -> 238, 864, 924, 1248, 2207 A -> G 429,800, 975, 1021, 1689, 1925, 2266, 3232, 3244 A -> T 492, 732, 1957 C ->500, 614, 634, 687, 701, 928, 1353, 2440 T -> A 615, 780 G -> C 818,2115 C -> G 819, 1612, 2210, 3333 T -> G 820, 3199, 3236 T -> C 820,1026, 3205 C -> A 1008, 3333 G -> T 1600, 3325 A -> 1955

The coding portion of transcript HUMSP18A_T30 (SEQ ID NO:120) starts atposition 137 and ends at position 1057. The transcript also has thefollowing SNPs as listed in Table 149 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HUMSP18A_P38 (SEQ IDNO:130) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 149 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1176, 1324, 3395,3472, A -> C 105, 2792 T -> 146 C -> T 180, 208, 466, 528, 662, 979,1975, 2107, 2216, 2481, 3359, 3416 G -> 238, 864, 924, 1248, 2377 A -> G429 A -> T 492 C -> 500, 614, 634, 687, 701, 928, 1523, 2610 T -> A 615,780, A -> T 732, 2127 A -> G 800, 975, 1021, 1859, 1975, 2436, 3402,3414 G -> C 818, 2285 C -> G 819, 1782, 2380, 3503 T -> G 820, 3369,3406 T -> C 820, 1026, 3375 C -> A 1008, 3503 1026 G -> T 1770, 3495 A-> 2125 G -> A 3285

Variant protein HUMSP18A_P39 (SEQ ID NO:131) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T15 (SEQ ID NO:115)and HUMSP18A_T27 (SEQ ID NO:118). An alignment is given to the knownprotein (Pulmonary surfactant-associated protein B precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMSP18A_P39 (SEQ ID NO:131) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P39 (SEQ IDNO:131), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREK corresponding to amino acids1-334 of PSPB_HUMAN (SEQ ID NO:406), which also corresponds to aminoacids 1-334 of HUMSP18A_P39 (SEQ ID NO:131), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequence LAPVC (SEQ ID NO: 484)corresponding to amino acids 335-339 of HUMSP18A_P39 (SEQ ID NO:131),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P39(SEQ ID NO:131), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence LAPVC (SEQ ID NO: 484) of HUMSP18A_P39 (SEQID NO:131).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P39 (SEQ ID NO:131) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table150, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P39 (SEQ ID NO:131) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 150 Amino acid mutations SNP position(s) on amino acid Alternativesequence amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R 119Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F 184 A-> 189 P -> 199 Q -> L 208 C -> Y 215 I -> N 222 I -> V 228 A -> G 228 A-> P 243 G -> 243 G -> D 263 G -> 264 R -> 272 R -> H 280 D -> G 290 G-> R 314 E -> 339 C -> Y

The glycosylation sites of variant protein HUMSP18A_P39 (SEQ ID NO:131),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 151 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 151 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 129Yes 129 311 Yes 311

Variant protein HUMSP18A_P39 (SEQ ID NO:131) is encoded by the followingtranscript(s): HUMSP18A_T15 (SEQ ID NO:115) and HUMSP18A_T27 (SEQ IDNO:118), for which the sequence(s) is/are given at the end of theapplication.

The coding portion of transcript HUMSP18A_T15 (SEQ ID NO:115) starts atposition 137 and ends at position 1153. The transcript also has thefollowing SNPs as listed in Table 152 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HUMSP18A_P39 (SEQ IDNO:131) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 152 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1004, 1152, 3113,3223, 3300 A -> C 105, 2620 T -> 146 C -> T 180, 208, 466, 528, 662,979, 1803, 1935, 2044, 2309, 3187, 3244 G -> 238, 864, 924, 1076, 2205 A-> G 429 A -> T 492, 732, 1955 C -> 500, 614, 634, 687, 701, 928, 1351,2438 T -> A 615, 780, A -> G 800, 975, 1687, 1923, 2264, 3230, 3242 G ->C 818, 2113 C -> G 819, 1610, 2208, 3331 T -> G 820, 3197, 3234 T -> C820, 3203 G -> T 1598, 3323 A -> 1953 C -> A 3331

The coding portion of transcript HUMSP18A_T27 (SEQ ID NO:118) starts atposition 137 and ends at position 1153. The transcript also has thefollowing SNPs as listed in Table 153 (given according to their positionon the nucleotide sequence, with the alternative nucleic acid listed;the presence of known SNPs in variant protein HUMSP18A_P39 (SEQ IDNO:131) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 153 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 951, 1004, 1152, 2286, 2473,864, 2396 A -> C 105, 1793 T -> 146 C -> T 180, 208, 466, 662, 979,1482, 2360, 2417 G -> 238, 864, 924, 1076 A -> G 429, 800, 975, 2403,2415 A -> T 492, 732 C -> 500, 614, 634, 687, 701, 928, 1351, 1611 C ->T 528 T -> A 615, 780 G -> C 818 C -> G 819, 2504 T -> G 820, 2370, 2407T -> C 820, 2376 G -> T 2496 C -> A 2504

Variant protein HUMSP18A_P41 (SEQ ID NO:132) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T20 (SEQ IDNO:116). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison report between HUMSP18A_P41 (SEQ ID NO:132) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P41 (SEQ IDNO:132), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIV LNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPK corresponding to amino acids 1-224 of PSPB_HUMAN (SEQ ID NO:406),which also corresponds to amino acids 1-224 of HUMSP18A_P41 (SEQ IDNO:132), and a second amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequenceVRHPGPHRAQEHTHTCSSLQLPPLSQLTPPSGPSWLPEVRRGESRLCIAPTQGTLGLRLRPGRCQAYSSCNKH(SEQ ID NO: 485) corresponding to amino acids 225-297 of HUMSP18A_P41(SEQ ID NO:132), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P41(SEQ ID NO:132), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceVRBPGPHRAQEHTHTCSSLQLPPLSQLTPPSGPSWLPEVRRGESRLCIAPTQGTLGLRLRPGRCQAYSSCNKH(SEQ ID NO:485) of HUMSP18A_P41 (SEQ ID NO:132).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P41 (SEQ ID NO:132) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table154, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P41 (SEQ ID NO:132) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 154 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R119 Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F184 A -> 189 P -> 199 Q -> L 208 C -> Y 215 I -> N 222 I -> V

The glycosylation sites of variant protein HUMSP18A_P41 (SEQ ID NO:132),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 155 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 155 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 129 Yes 129311 No

Variant protein HUMSP18A_P41 (SEQ ID NO:132) is encoded by the followingtranscript(s): HUMSP18A_T20 (SEQ ID NO:116), for which the codingportion starts at position 137 and ends at position 1027. The transcriptalso has the following SNPs as listed in Table 156 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P41(SEQ ID NO:132) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 156 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 1060, 1643, 2007, 2305, 2392,2445, 4384, 4494, 4571 A -> C 105, 3891 T -> 146 C -> T 180, 208, 466,528, 662, 2218, 2420, 3074, 3206, 3315, 3580, 4458, 4515 G -> 238, 2305,2365, 2517, 3476 A -> G 429, 800, 2416, 2958, 3194, 3535, 4501, 4513 A-> T 492, 732, 1334, 3226 C -> 500, 614, 634, 687, 701, 2369, 2622, 3709T -> A 615, 780 A -> 1841, 3224 G -> C 1956, 2259, 3384 T -> C 2066,2261, 4474 C -> G 2260, 2882, 3479, 4602 T -> G 2261, 4468, 4505 G -> T2869, 4594 C -> A 4602

Variant protein HUMSP18A_P43 (SEQ ID NO:133) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T23 (SEQ ID NO:17).An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P43 (SEQ ID NO:133) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P43 (SEQ IDNO:133), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTcorresponding to amino acids 1-131 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 1-131 of HUMSP18A_P43 (SEQ ID NO:133),and a second amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceVRAASSPPACLPTQAPVPTHGEPHTQBPSQPDTHTHITHTAPKPARHKHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHTHTQBPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHTHSTPAGHMTH™THPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTHPYTLTLTHMLTBLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) corresponding to amino acids 132-360 ofHUMSP18A_P43 (SEQ ID NO:133), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P43(SEQ ID NO:133), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceVRAASSPPACLPTQAPVPTHGEPHTQHPSQPDTHTHTHTHTAPKPARHEHTAPQPAGHTHTHTHNTPAGRTHTHTVPQLAGHTHTQHPIQTHTHTQYPSQLETHTHTALHPDTYPHSTPASQTHTHTHTHTHTQHTHSTPAGHTHTHTEPVHKGPRKLRALQPCTRPWAPRFRCTRWACTLTBPYTLTLTHMLTHLFILTYMLMLIHTQSRPPALKSPHSPIFAFCPPT (SEQ ID NO: 482) of HUMSP18A_P43 (SEQ ID NO:133).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P43 (SEQ ID NO:133) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table157, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P43 (SEQ ID NO:133) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 157 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R119 Y -> F 122 L -> 131 T -> I 265 Q -> E

The glycosylation sites of variant protein HUMSP18A_P43 (SEQ ID NO:133),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 158 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 158 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 129 Yes 129311 No

Variant protein HUMSP18A_P43 (SEQ ID NO:133) is encoded by the followingtranscript(s): HUMSP18A_T23 (SEQ ID NO:117), for which the codingportion starts at position 137 and ends at position 1216. The transcriptalso has the following SNPs as listed in Table 159 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P43(SEQ ID NO:133) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 159 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 1581, 1686, 1773, 1826, 3765, 3875,3952 A -> C 105, 3272 T -> 146 C -> T 180, 208, 528, 1484, 1801, 2455,2587, 2696, 2961, 3839, 3896 G -> 238, 1686, 1746, 1898, 2857 A -> G429, 622, 1622, 1797, 2339, 2575, 2916, 3882, 3894 C -> T 466 A -> T492, 1554, 2607 C -> 500, 1436, 1456, 1509, 1523, 1750, 2003, 3090 C ->G 929, 1641, 2262, 2860, 3983 T -> A 1437, 1602 G -> C 1640, 2765 T -> G1642, 3849, 3886 T -> C 1642, 3855 G -> T 2250, 3975 A -> 2605 C -> A3983

Variant protein HUMSP18A_P45 (SEQ ID NO:134) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T29 (SEQ IDNO:119). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P45 (SEQ ID NO:134) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P45 (SEQ IDNO:134), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGAcorresponding to amino acids 1-65 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 1-65 of HUMSP18A_P45 (SEQ ID NO:134), asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceRTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO: 487) corresponding to amino acids66-89 of HUMSP18A_P45 (SEQ ID NO:134), and a third amino acid sequencebeing at least 90% homologous toDDLCQECEDWHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREKCKQFVEQHTPQLLTLVPRGWDAHTTCQALGVCGTMSSPLQCIHSPDL corresponding to amino acids 66-381 of PSPB_HUMAN(SEQ ID NO:406), which also corresponds to amino acids 90-405 ofHUMSP18A_P45 (SEQ ID NO:134), wherein said first amino acid sequence,second amino acid sequence and third amino acid sequence are contiguousand in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P45(SEQ ID NO:134), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence RTSPLELGASPTHVSSTLGPLPPQ (SEQ ID NO: 487) ofHUMSP18A_P45 (SEQ ID NO:134).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P45 (SEQ ID NO:134) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table160, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P45 (SEQ ID NO:134) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 160 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 87 P -> H122 Q -> R 143 Y -> F 146 L -> 155 T -> I 184 L -> 184 L -> Q 190 D ->200 L -> F 208 A -> 213 P -> 223 Q -> L 232 C -> Y 239 I -> N 246 I -> V252 A -> G 252 A -> P 267 G -> 267 G -> D 287 G -> 288 R -> 296 R -> H304 D -> G 314 G -> R 338 E -> 373 L ->

The glycosylation sites of variant protein HUMSP18A_P45 (SEQ ID NO:134),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 161 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 161 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 153 Yes 153335 Yes 335

Variant protein HUMSP18A_P45 (SEQ ID NO:134) is encoded by the followingtranscript(s): HUMSP18A_T29 (SEQ ID NO:119), for which the codingportion starts at position 137 and ends at position 1351. The transcriptalso has the following SNPs as listed in Table 162 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P45(SEQ ID NO:134) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 162 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 499, 831, 936, 1023, 1076, 3015, 3125,3202 A -> C 105, 2522 T -> 146 C -> T 180, 208, 538, 600, 734, 1051,1705, 1837, 1946, 2211, 3089, 3146 G -> 238, 936, 996, 1148, 2107 C -> A396, 3233 A -> G 501, 872, 1047, 1589, 1825, 2166, 3132, 3144 A -> T564, 804, 1857 C -> 572, 686, 759, 706, 773, 1000, 2340, 1253 T -> A687, 852 G -> C 890, 2015 C -> G 891, 1512, 2110, 3233 T -> G 892, 3099,3136 T -> C 892, 3105 G -> T 1500, 3225 A -> 1855

Variant protein HUMSP18A_P48 (SEQ ID NO:135) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T34 (SEQ IDNO:121). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P48 (SEQ ID NO:135) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P48 (SEQ IDNO:135), comprising a first amino acid sequence being at least 90%homologous toMAESBLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIRJQA MIPKG corresponding to amino acids 1-225 of PSPB_HUMAN (SEQ IDNO:406), which also corresponds to amino acids 1-225 of HUMSP18A_P48(SEQ ID NO:135), and a second amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95% homologous to a polypeptidehaving the sequence RRQENGCRETLSATSACP (SEQ ID NO: 488) corresponding toamino acids 226-243 of HUMSP18A_P48 (SEQ ID NO:135), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P48(SEQ ID NO:135), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence RRQENGCRETLSATSACP (SEQ ID NO: 488) ofHUMSP18A_P48 (SEQ ID NO:135).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P48 (SEQ ID NO:135) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table163, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P48 (SEQ ID NO:135) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 163 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R119 Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F184 A -> 189 P -> 199 Q -> L 208 C -> Y 215 I -> N 222 I -> V

The glycosylation sites of variant protein HUMSP18A_P48 (SEQ ID NO:135),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 164 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 164 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 129 Yes 129311 No

Variant protein HUMSP18A_P48 (SEQ ID NO:135) is encoded by the followingtranscript(s): HUMSP18A_T34 (SEQ ID NO:121), for which the codingportion starts at position 137 and ends at position 865. The transcriptalso has the following SNPs as listed in Table 165 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P48(SEQ ID NO:135) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 165 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 820, 2869, 2946 A -> C 105, 2266T -> 146 C -> T 180, 208, 466, 528, 662, 1449, 1581, 1690, 1955, 2833,2890 G -> 238, 892, 1851 A -> G 429, 800, 1333, 1569, 1910, 2876, 2888 A-> T 492, 732, 1601 C -> 500, 614, 634, 687, 701, 997, 2084 T -> A 615,780 G -> T 1244, 2969 C -> G 1256, 1854, 2977 A -> 1599 G -> C 1759 G ->A 2759 T -> G 2843, 2880 T -> C 2849 C -> A 2977

Variant protein HUMSP18A_P49 (SEQ ID NO:136) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T35 (SEQ IDNO:122). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P49 (SEQ ID NO:136) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P49 (SEQ IDNO:136), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREKCKQFVEQHTPQLLTLVPRGWDAHITCQcorresponding to amino acids 1-361 of PSPB_HUMAN (SEQ ID NO:406), whichalso corresponds to amino acids 1-361 of HUMSP18A_P49 (SEQ ID NO:136),and a second amino acid sequence being at least 70%, optionally at least80%, preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceKKTPSFKVLQYGQTWWLTPAIPAP (SEQ ID NO: 489) corresponding to amino acids362-385 of HUMSP18A_P49 (SEQ ID NO:136), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of HUMSP18A_P49(SEQ ID NO:136), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence KKTPSFKVLQYGQTWWLTPAIPAP (SEQ ID NO: 489) ofHUMSP18A_P49 (SEQ ID NO:136).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P49 (SEQ ID NO:136) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table166, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P49 (SEQ ID NO:136) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 166 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R119 Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F184 A -> 189 P -> 199 Q -> L 208 C -> Y 215 I -> N 222 I -> V 228 A -> G228 A -> P 243 G -> 243 G -> D 263 G -> 264 R -> 272 R -> H 280 D -> G290 G -> R 314 E -> 349 L -> 365 P -> L

The glycosylation sites of variant protein HUMSP18A_P49 (SEQ ID NO:136),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 167 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 167 Glycosylation site(s) Position(s) on known Position(s) aminoacid sequence Present in variant protein? on variant protein 129 Yes 129311 Yes 311

Variant protein HUMSP18A_P49 (SEQ ID NO:136) is encoded by the followingtranscript(s): HUMSP18A_T35 (SEQ ID NO:122), for which the codingportion starts at position 137 and ends at position 1291. The transcriptalso has the following SNPs as listed in Table 168 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P49(SEQ ID NO:136) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 168 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence G -> A 95, 184, 316, 427, 759, 864, 951, 1004, 2034, 2144, 2221A -> C 105 T -> 146 C -> T 180, 208, 466, 528, 662 G -> 238, 864, 924,1076 A -> G 429, 800, 975, 2151, 2163 A -> T 492, 732 C -> 500, 614,634, 687, 701, 928, 1181, 1359 T -> A 615, 780, G -> C 818 C -> G 819,2252 T -> G 820, 2118, 2155 T -> C 820, 2124 C -> T 979, 1230, 2108,2165 A -> C 1541 G -> T 2244 C -> A 2252

Variant protein HUMSP18A_P50 (SEQ ID NO:137) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T38 (SEQ IDNO:123). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P50 (SEQ ID NO:137) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P50 (SEQ IDNO:137), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQDTMRKFLEQECNVLPLKLLMPQCNQVLDDYFPLVIDYFQNQTDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQ corresponding toamino acids 1-194 of PSPB_HUMAN (SEQ ID NO:406), which also correspondsto amino acids 1-194 of HUMSP18A_P50 (SEQ ID NO:137), and a second aminoacid sequence being at least 90% homologous toGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREKCKQFVEQHTPQLLTLVPRGWDAHTTCQALGVCGTMSSPLQCIHSPDL corresponding to amino acids 225-381 of PSPB_HUMAN (SEQ IDNO:406), which also corresponds to amino acids 195-351 of HUMSP18A_P50(SEQ ID NO:137), wherein said first amino acid sequence and second aminoacid sequence are contiguous and in a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHUMSP18A_P50 (SEQ ID NO:137), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise QG, having a structure as follows: asequence starting from any of amino acid numbers 194−x to 194; andending at any of amino acid numbers 195+((n−2)−x), in which x variesfrom 0 to n−2.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P50 (SEQ ID NO:137) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table169, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P50 (SEQ ID NO:137) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 169 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 98 Q -> R 119Y -> F 122 L -> 131 T -> I 160 L -> 160 L -> Q 166 D -> 176 L -> F 184 A-> 189 P -> 198 A -> G 198 A -> P 213 G -> 213 G -> D 233 G -> 234 R ->242 R -> H 250 D -> G 260 G -> R 284 E -> 319 L ->

The glycosylation sites of variant protein HUMSP18A_P50 (SEQ ID NO:137),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 170 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 170 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 129Yes 129 281 Yes 281

Variant protein HUMSP18A_P50 (SEQ ID NO:137) is encoded by the followingtranscript(s): HUMSP18A_T38 (SEQ ID NO:123), for which the codingportion starts at position 137 and ends at position 1189. The transcriptalso has the following SNPs as listed in Table 171 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P50(SEQ ID NO:137) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 171 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence G -> A 95, 184, 316, 427, 774, 861, 914, 2853, 2963, 3040 A ->C 105, 2360 T -> 146 C -> T 180, 466, 528, 662, 889, 1675, 2927, 2984,1784, 208, 1543 G -> 238, 774, 986, 834, 1945 A -> G 429, 1427, 885,1663, 2004, 2970, 2982 A -> T 492, 1695 C -> 500, 614, 687, 634, 701,838, 1091, 2178 T -> A 615 G -> C 728, 1853 C -> G 729, 1350, 1948, 3071T -> G 730, 2937, 2974 T -> C 730, 2943 G -> T 1338, 3063 A -> 1693 C ->T 2049 C -> A 3071

Variant protein HUMSP18A_P53 (SEQ ID NO:138) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMSP18A_T42 (SEQ IDNO:124). An alignment is given to the known protein (Pulmonarysurfactant-associated protein B precursor) in the alignment table on theattached CD-ROM. A brief description of the relationship of the variantprotein according to the present invention to each such aligned proteinis as follows:

1. Comparison Report Between HUMSP18A_P53 (SEQ ID NO:138) and PSPB_HUMAN(SEQ ID NO:406):

A. An isolated chimeric polypeptide as set forth in HUMSP18A_P53 (SEQ IDNO:138), comprising a first amino acid sequence being at least 90%homologous toMAESHLLQWLLLLLPTLCGPGTAAWTTSSLACAQGPEFWCQSLEQALQCRALGHCLQEVWGHVGADDLCQECEDIVHILNKMAKEAIFQ corresponding to amino acids 1-89 of PSPB_HUMAN (SEQID NO:406), which also corresponds to amino acids 1-89 of HUMSP18A_P53(SEQ ID NO:138), and a second amino acid sequence being at least 90%homologous toDSNGICMHLGLCKSRQPEPEQEPGMSDPLPKPLRDPLPDPLLDKLVLPVLPGALQARPGPHTQDLSEQQFPIPLPYCWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCSMDDSAGPRSPTGEWLPRDSECHLCMSVTTQAGNSSEQAIPQAMLQACVGSWLDREKCKQFVEQHTPQLLTLVPRGWDAHTTCQALGVCGTMSSPLQCIHSPDL corresponding to amino acids 132-381 ofPSPB_HUMAN (SEQ ID NO:406), which also corresponds to amino acids 90-339of HUMSP18A_P53 (SEQ ID NO:138), wherein said first amino acid sequenceand second amino acid sequence are contiguous and in a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHUMSP18A_P53 (SEQ ID NO:138), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise QD, having a structure as follows: asequence starting from any of amino acid numbers 89−x to 89; and endingat any of amino acid numbers 90+((n−2)−x), in which x varies from 0 ton−2.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMSP18A_P53 (SEQ ID NO:138) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table172, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMSP18A_P53 (SEQ ID NO:138) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 172 Amino acid mutations SNP position(s) on Alternative amino acidsequence amino acid(s) 4 S -> 15 P -> L 34 Q -> 60 W -> * 118 L -> 118 L-> Q 124 D -> 134 L -> F 142 A -> 147 P -> 157 Q -> L 166 C -> Y 173 I-> N 180 I -> V 186 A -> G 186 A -> P 201 G -> 201 G -> D 221 G -> 222 R-> 230 R -> H 238 D -> G 248 G -> R 272 E -> 307 L ->

The glycosylation sites of variant protein HUMSP18A_P53 (SEQ ID NO:138),as compared to the known protein Pulmonary surfactant-associated proteinB precursor, are described in Table 173 (given according to theirposition(s) on the amino acid sequence in the first column; the secondcolumn indicates whether the glycosylation site is present in thevariant protein; and the last column indicates whether the position isdifferent on the variant protein).

TABLE 173 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 129No 269 Yes 269

Variant protein HUMSP18A_P53 (SEQ ID NO:138) is encoded by the followingtranscript(s): HUMSP18A_T42 (SEQ ID NO:124), for which the codingportion starts at position 137 and ends at position 1153. The transcriptalso has the following SNPs as listed in Table 174 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMSP18A_P53(SEQ ID NO:138) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 174 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence G -> A 95, 184, 633, 316, 738, 878, 2927, 2817, 825, 3004 A ->C 105, 2324 T -> 146 C -> T 180, 208, 536, 853, 1748, 1507, 2013, 2891,2948, 1639 G -> 238, 738, 1909, 950, 798 C -> 488, 561, 508, 575, 802,1055, 2142 T -> A 489, 654 A -> T 606, 1659 A -> G 674, 849, 1391, 1627,1968, 2934, 2946 G -> C 692, 1817 C -> G 693, 1314, 1912, 3035 T -> G694, 2901, 2938 T -> C 694, 2907 G -> T 1302, 3027 A -> 1657 C -> A 3035

As noted above, cluster HUMSP18A features 50 segment(s), which werelisted in Table 132 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segments 32, 34, and 38 according to the present invention is nowprovided.

Segment cluster HUMSP18A_N32 (SEQ ID NO:164) according to the presentinvention is supported by 16 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMSP18A_T14 (SEQ ID NO:114) and HUMSP18A_T30(SEQ ID NO:120). Table 175 below describes the starting and endingposition of this segment on each transcript.

TABLE 175 Segment location on transcripts Segment Segment startingending Transcript name position position HUMSP18A_T14 (SEQ ID NO: 114)993 1164 HUMSP18A_T30 (SEQ ID NO: 120) 993 1164

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster HUMSP18A_N34 (SEQ ID NO:166) according to the presentinvention is supported by 89 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMSP18A_T14 (SEQ ID NO:114), HUMSP18A_T15 (SEQID NO:115), HUMSP18A_T20 (SEQ ID NO:116), HUMSP18A_T23 (SEQ ID NO:117),HUMSP18A_T27 (SEQ ID NO:118), HUMSP18A_T29 (SEQ ID NO:119), HUMSP18A_T30(SEQ ID NO:120), HUMSP18A_T34 (SEQ ID NO:121), HUMSP18A_T35 (SEQ IDNO:122), HUMSP18A_T38 (SEQ ID NO:123), HUMSP18A_T42 (SEQ ID NO:124),HUMSP18A_T44 (SEQ ID NO:125) and HUMSP18A_T46 (SEQ ID NO:126). Table 176below describes the starting and ending position of this segment on eachtranscript.

TABLE 176 Segment location on transcripts Segment Segment startingending Transcript name position position HUMSP18A_T14 (SEQ ID NO: 114)1177 1208 HUMSP18A_T15 (SEQ ID NO: 115) 1005 1036 HUMSP18A_T20 (SEQ IDNO: 116) 2446 2477 HUMSP18A_T23 (SEQ ID NO: 117) 1827 1858 HUMSP18A_T27(SEQ ID NO: 118) 1005 1036 HUMSP18A_T29 (SEQ ID NO: 119) 1077 1108HUMSP18A_T30 (SEQ ID NO: 120) 1177 1208 HUMSP18A_T34 (SEQ ID NO: 121)821 852 HUMSP18A_T35 (SEQ ID NO: 122) 1005 1036 HUMSP18A_T38 (SEQ ID NO:123) 915 946 HUMSP18A_T42 (SEQ ID NO: 124) 879 910 HUMSP18A_T44 (SEQ IDNO: 125) 928 959 HUMSP18A_T46 (SEQ ID NO: 126) 1750 1781

Segment cluster HUMSP18A_N38 (SEQ ID NO:170) according to the presentinvention is supported by 79 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMSP18A_T14 (SEQ ID NO:114), HUMSP18A_T15 (SEQID NO:115), HUMSP18A_T20 (SEQ ID NO:116), HUMSP18A_T23 (SEQ ID NO:117),HUMSP18A_T27 (SEQ ID NO:118), HUMSP18A_T29 (SEQ ID NO:119), HUMSP18A_T30(SEQ ID NO:120), HUMSP18A_T34 (SEQ ID NO:121), HUMSP18A_T35 (SEQ IDNO:122), HUMSP18A_T38 (SEQ ID NO:123), HUMSP18A_T42 (SEQ ID NO:124),HUMSP18A_T44 (SEQ ID NO:125) and HUMSP18A_T46 (SEQ ID NO:126). Table 177below describes the starting and ending position of this segment on eachtranscript.

TABLE 177 Segment location on transcripts Segment Segment startingending Transcript name position position HUMSP18A_T14 (SEQ ID NO: 114)1290 1295 HUMSP18A_T15 (SEQ ID NO: 115) 1118 1123 HUMSP18A_T20 (SEQ IDNO: 116) 2559 2564 HUMSP18A_T23 (SEQ ID NO: 117) 1940 1945 HUMSP18A_T27(SEQ ID NO: 118) 1118 1123 HUMSP18A_T29 (SEQ ID NO: 119) 1190 1195HUMSP18A_T30 (SEQ ID NO: 120) 1290 1295 HUMSP18A_T34 (SEQ ID NO: 121)934 939 HUMSP18A_T35 (SEQ ID NO: 122) 1118 1123 HUMSP18A_T38 (SEQ ID NO:123) 1028 1033 HUMSP18A_T42 (SEQ ID NO: 124) 992 997 HUMSP18A_T44 (SEQID NO: 125) 1041 1046 HUMSP18A_T46 (SEQ ID NO: 126) 1863 1868

FIG. 22 shows the structure of the mRNA and protein variants of clusterHUMSP18A. “WT” refers to the known protein/mRNA.

Expression of Homo sapiens Surfactant, Pulmonary-Associated Protein B(SFTPB), Transcript Variant 2 HUMSP18A Transcripts which are Detectableby Amplicon as Depicted in Sequence Name HUMSP18A seg32 (SEQ ID NO: 407)in Normal and Cancerous Lung Tissues

Expression of Homo sapiens surfactant, pulmonary-associated protein B(SFTPB), transcript variant 2 transcripts detectable by or according toseg32, HUMSP18A seg32 amplicon (SEQ ID NO: 407) and primers HUMSP18Aseg32F (SEQ ID NO: 408) and HUMSP18A seg32R (SEQ ID NO: 409) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes —PBGD (GenBank Accession No. BC019323 (SEQ IDNO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), Ubiquitin (GenBank Accession No. BC000449 (SEQ IDNO:366); amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) and SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), was measured similarly. For each RT sample, the expressionof the above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (Sample Nos. 47-50, 90-93, 96-99, Table 3).Then the reciprocal of this ratio was calculated, to obtain a value offold down-regulation for each sample relative to median of the normal PMsamples.

FIG. 23 is a histogram showing down regulation of the above-indicatedHomo sapiens surfactant, pulmonary-associated protein B (SFTPB),transcript variant 2 transcripts (seg32) in cancerous lung samplesrelative to the normal samples.

As is evident from FIG. 23, the expression of Homo sapiens surfactant,pulmonary-associated protein B (SFTPB), transcript variant 2 transcriptsdetectable by the above amplicon in cancer samples was significantlylower than in the non-cancerous samples (Sample Nos. 46-50, 90-93, 96-99Table 3). Notably down regulation of at least 10 fold was found in 8 outof 16 squamous cell carcinoma samples, 3 out of 4 large cell carcinomasamples and in 8 out of 8 small cells carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssurfactant, pulmonary-associated protein B (SFTPB), transcript variant 2transcripts detectable by the above amplicon in lung cancer samplesversus the normal tissue samples was determined by T test as 8.99E-02 insquamous cell carcinoma, and 1.2E-02 in Small cell carcinoma.

Threshold of 10 fold down regulation was found to differentiate betweencancer and normal samples with P value of 4.14E-03 in Squamous cellcarcinoma, 7.14E-03 in Large cell carcinoma and 7.94E-06 in Small cellcarcinoma as checked by exact fisher test. The above values demonstratestatistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HUMSP18A seg32F (SEQ ID NO: 408) forward primer;and HUMSP18A seg32R (SEQ ID NO: 409) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HUMSP18A seg32 (SEQ IDNO: 407).

Forward primer HUMSP18A seg32F (SEQ ID NO: 408): CCCACTGCCCCCTCCTTReverse primer HUMSP18A seg32R (SEQ ID NO: 409): TGGTTTCTGTCCTCCTTGGTGAmplicon HUMSP18A seg32 (SEQ ID NO: 407):CCCACTGCCCCCTCCTTAGCCCAATGCCTGCTCTCCTCCTCCCCCTACCCTGCCACTGCATGACCCTCTCCCTCTGTGGTCCCACTGCAATGCACCAAGG AGGACAGAAACCAExpression of Homo sapiens Surfactant, Pulmonary-Associated Protein B(SFTPB) HUMSP18A Transcripts which are Detectable by Amplicon asDepicted in Sequence Name HUMSP18A_seg32 (SEQ ID NO: 407) in DifferentNormal Tissues

Expression of Homo sapiens surfactant, pulmonary-associated protein B(SFTPB) transcripts detectable by or according to seg32—HUMSP18A_seg32(SEQ ID NO: 407) amplicon and primers HUMSP18A_seg32F (SEQ ID NO: 408)and HUMSP18A_seg32R (SEQ ID NO: 409) was measured by real time PCR. Inparallel the expression of four housekeeping genes—SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)), RPL19 (GenBank AccessionNo. NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon) andTATA box (GenBank Accession No. NM_(—)003194 (SEQ ID NO:371); TATA (SEQID NO:370) amplicon) was measured similarly. For each RT sample, theexpression of the above amplicon was normalized to the geometric mean ofthe quantities of the housekeeping genes. The normalized quantity ofeach RT sample was then divided by the median of the quantities of thelung samples (sample numbers 15, 16 and 17, Table 5 above), to obtain avalue of relative expression of each sample relative to median of thelung samples. FIG. 24 shows expression of Homo sapiens surfactant,pulmonary-associated protein B (SFTPB) transcripts detectable by oraccording to seg32 in normal tissues.

Forward primer (HUMSP18A_seg32F (SEQ ID NO: 408)): CCCACTGCCCCCTCCTTReverse primer (HUMSP18A_seg32R (SEQ ID NO: 409)): TGGTTTCTGTCCTCCTTGGTGAmplicon (HUMSP18A_seg32 (SEQ ID NO: 407)):CCCACTGCCCCCTCCTTAGCCCAATGCCTGCTCTCCTCCTCCCCCTACCCTGCCACTGCATGACCCTCTCCCTCTGTGGTCCCACTGCAATGCACCAAGG AGGACAGAAACCAExpression of Homo sapiens Surfactant, Pulmonary-Associated Protein B(SFTPB), Transcript Variant 2 HUMSP18A Transcripts which are Detectableby Amplicon as Depicted in Sequence Name HUMSP18A seg34-38WT (SEQ ID NO:410) in Normal and Cancerous Lung Tissues

Expression of Homo sapiens surfactant, pulmonary-associated protein B(SFTPB), transcript variant 2 transcripts detectable by or according toseg34-38, HUMSP18A seg34-38WT amplicon (SEQ ID NO: 410) and primersHUMSP18A seg34-38WTF (SEQ ID NO: 411) and HUMSP18A seg34-38WTR (SEQ IDNO: 412) was measured by real time PCR. In parallel the expression offour housekeeping genes —PBGD (GenBank Accession No. BC019323 (SEQ IDNO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), Ubiquitin (GenBank Accession No. BC000449 (SEQ IDNO:366); amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) and SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), was measured similarly. For each RT sample, the expressionof the above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (Sample Nos. 47-50, 90-93, 96-99, Table 3).Then the reciprocal of this ratio was calculated, to obtain a value offold down-regulation for each sample relative to median of the normal PMsamples.

FIG. 25 is a histogram showing down regulation of the above-indicatedHomo sapiens surfactant, pulmonary-associated protein B (SFTPB),transcript variant 2 transcripts in cancerous lung samples relative tothe normal samples (seg34-38WT).

As is evident from FIG. 25, the expression of Homo sapiens surfactant,pulmonary-associated protein B (SFTPB), transcript variant 2 transcriptsdetectable by the above amplicon in cancer samples was significantlylower than in the non-cancerous samples (Sample Nos. 46-50, 90-93, 96-99Table 3). Notably down regulation of at least 10 fold was found in 9 outof 16 squamous cell carcinoma samples, 3 out of 4 large cell carcinomasamples and in 8 out of 8 small cells carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssurfactant, pulmonary-associated protein B (SFTPB), transcript variant 2transcripts detectable by the above amplicon in lung cancer samplesversus the normal tissue samples was determined by T test as 5.64E-03 inSmall cell carcinoma.

Threshold of 10 fold down regulation was found to differentiate betweencancer and normal samples with P value of 1.66E-03 in Squamous cellcarcinoma, 7.14E-03 in Large cell carcinoma and 7.94E-06 in Small cellcarcinoma as checked by exact fisher test. The above values demonstratestatistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: HUMSP18A seg34-38WTF (SEQ ID NO: 411) forwardprimer; and HUMSP18A seg34-38WTR (SEQ ID NO: 412) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: HUMSP18A seg34-38WT(SEQ ID NO: 410).

Forward primer HUMSP18A seg34-38WTF (SEQ ID NO: 411): GAGAATGGCTGCCGCGReverse primer HUMSP18A seg34-38WTR (SEQ ID NO: 412):CATTGCCTGTGGTATGGCCT Amplicon HUMSP18A seg34-38WT (SEQ ID NO: 410):GAGAATGGCTGCCGCGAGACTCTGAGTGCCACCTCTGCAGTCCGTGACCACCCAGGCCGGGAACAGCAGCGAGCAGGCCATACCACAGGCAATGExpression of Homo sapiens Surfactant, Pulmonary-Associated Protein B(SFTPB) HUMSP18A Transcripts which are Detectable by Amplicon asDepicted in Sequence Name HUMSP18A_seg34-38WT (SEQ ID NO: 410) inDifferent Normal Tissues

Expression of Homo sapiens surfactant, pulmonary-associated protein B(SFTPB) transcripts detectable by or according toseg34-38WT—HUMSP18A_seg34-38WT (SEQ ID NO: 410) amplicon and primersHUMSP18A_seg34-38WTF (SEQ ID NO: 411) and HUMSP18A_seg34-38WTR (SEQ IDNO: 412) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369)RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371) TATA (SEQ ID NO:370) amplicon) was measuredsimilarly. For each RT sample, the expression of the above amplicon wasnormalized to the geometric mean of the quantities of the housekeepinggenes. The normalized quantity of each RT sample was then divided by themedian of the quantities of the lung samples (sample numbers 15, 16 and17, Table 5 above), to obtain a value of relative expression of eachsample relative to median of the lung samples. FIG. 26 shows the resultsof expression of Homo sapiens surfactant, pulmonary-associated protein B(SFTPB) transcripts detectable by or according to seg34-38WT on a normalpanel.

Forward primer (HUMSP18A_seg34-38WTF (SEQ ID NO: 411)): GAGAATGGCTGCCGCGReverse primer (HUMSP18A_seg34-38WTR (SEQ ID NO: 412)):CATTGCCTGTGGTATGGCCT Amplicon HUMSP18A_seg34-38WT (SEQ ID NO: 410):GAGAATGGCTGCCGCGAGACTCTGAGTGCCACCTCTGCAGTCCGTGACCACCCAGGCCGGGAACAGCAGCGAGCAGGCCATACCACAGGCAATG

Description for Cluster F05068

Cluster F05068 features 4 transcript(s) and 15 segment(s) of interest,the names for which are given in Tables 178 and 179, respectively. Theselected protein variants are given in table 180.

TABLE 178 Transcripts of interest Transcript Name F05068_T6 (SEQ ID NO:189) F05068_T7 (SEQ ID NO: 190) F05068_T8 (SEQ ID NO: 191) F05068_T9(SEQ ID NO: 192)

TABLE 179 Segments of interest Segment Name F05068_N0 (SEQ ID NO: 196)F05068_N5 (SEQ ID NO: 199) F05068_N9 (SEQ ID NO: 203) F05068_N13 (SEQ IDNO: 207) F05068_N15 (SEQ ID NO: 209) F05068_N16 (SEQ ID NO: 210)F05068_N3 (SEQ ID NO: 197) F05068_N4 (SEQ ID NO: 198) F05068_N6 (SEQ IDNO: 200) F05068_N7 (SEQ ID NO: 201) F05068_N8 (SEQ ID NO: 202)F05068_N10 (SEQ ID NO: 204) F05068_N11 (SEQ ID NO: 205) F05068_N12 (SEQID NO: 206) F05068_N14 (SEQ ID NO: 208)

TABLE 180 Proteins of interest Protein Name Corresponding Transcript(s)F05068_P6 (SEQ ID NO: 193) F05068_T9 (SEQ ID NO: 192) F05068_P9 (SEQ IDNO: 194) F05068_T6 (SEQ ID NO: 189); F05068_T7 (SEQ ID NO: 190)F05068_P10 (SEQ ID NO: 195) F05068_T8 (SEQ ID NO: 191)

These sequences are variants of the known protein ADM precursor(SwissProt accession identifier ADML_HUMAN (SEQ ID NO:413)), referred toherein as the previously known protein.

Protein ADM precursor is known or believed to have the followingfunction(s): AM and PAMP are potent hypotensive and vasodilatatoragents. Numerous actions have been reported most related to thephysiologic control of fluid and electrolyte homeostasis. In the kidney,am is diuretic and natriuretic, and both am and pamp inhibit aldosteronesecretion by direct adrenal actions. In pituitary gland, both peptidesat physiologically relevant doses inhibit basal ACTH secretion. Bothpeptides appear to act in brain and pituitary gland to facilitate theloss of plasma volume, actions which complement their hypotensiveeffects in blood vessels. The sequence for protein ADM precursor isgiven at the end of the application, as “ADM precursor amino acidsequence”. Known polymorphisms for this sequence are as shown in Table181.

TABLE 181 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 50 S -> R (in dbSNP: 5005). /FTId =VAR_014861

Protein ADM precursor localization is believed to be Secreted.

Adrenomedullin, a hypotensive peptide found in human pheochromocytoma,consists of 52 amino acids, has 1 intramolecular disulfide bond, andshows a slight homology with the calcitonin gene-related peptide. It mayfunction as a hormone in circulation control because it is found inblood in a considerable concentration. The precursor, calledpreproadrenomedullin, is 185 amino acids long. By RNA-blot analysis,human adrenomedullin mRNA was found to be highly expressed in severaltissues.

In the final step of production of adrenomedullin (AM), an inactiveintermediate form of glycine-extended AM (AM-glycine) is converted tothe active mature form of adrenomedullin (AM-mature) by enzymaticamidation. Recent studies have revealed that AM-mature and AM-glycinecirculate in human plasma.

According to optional embodiments of the present invention, the variantsof F05068 described below may optionally be in the form of “AMvariant-glycine”, in which the variant sequence features an additionalglycine residue at the N-terminus.

TABLE 182 Indication Reason reference Diagnosis of children with acutePlasma urinary adrenomedullin Clin Biochem. 2005 rheumatic fever andtotal nitrite levels were Jun; 38(6): 526-30. significantly higher inchildren with ARF, irrespective of whether they were in the acute orconvalescent phase of disease. Diagnosis and clinical The mean plasmaTumori. 2005 Jan-Feb; 91(1): 53-8. monitoring of adrenomedullinconcentration Horm Metab Res. 2001 pheochromocytoma, alone or in (+/−SD)in patients with May; 33(5): 290-4. combination with pheochromocytomas(27.5 +/− Cancer Detect Prev. chromogranin A 10.4 pg/mL) wassignificantly 1997; 21(1): 51-4. higher (P < 0.001) than that in HS(13.8 +/− 4.5 pg/mL) and in patients with non-functioning adrenocorticaladenomas (16.6 +/− 7.3 pg/mL). Plasma CgA levels correlated with plasmaadrenomedullin levels (r = 0.501; P < 0.02) and with plasma metanephrinelevels (r = 0.738; P < 0.0001) in patients with pheochromocytomas. In 11patients with pheochromocytomas plasma CgA and adrenomedullinconcentrations significantly decreased after tumor removal (P < 0.001for both). Diagnosis of vascular and The mean vitreous Ophthalmologica.2005 Mar-Apr; proliferative retinal diseases, adrenomedullin levels(63.9 +/− 219(2): 107-11. alone or in combination with 7.1 pmol/l) weresignificantly Am J Ophthalmol. 1999 leptin. higher (p < 0.05) inproliferative Dec; 128(6): 765-7. diabetic retinopathy patients than inpatients with other retinal diseases including macular hole andepiretinal membrane (34.25 +/− 3.0 pmol/l). predictor of patient (poor)Multivariate analysis identified Intern Med. 2004 prognosis in acutemyocardial only high levels of Nov; 43(11): 1015-22. infarction (AMI),alone or in adrenomedullin as an Angiology. 2005 Jan-Feb; combinationwith brain independent related factor of 56(1): 35-42. natriureticpeptide (BNP), atrial cardiogenic shock (risk ratio: Heart. 1998 Jan;79(1): 39-44 natriuretic peptide (ANP), renin, 5.84, 95% C.I.:1.80-18.95, aldosterone, adrenomedullin, p = 0.003), and as anindependent epinephrine and norepinephrine predictor of short-termmortality (risk ratio: 16.16, 95% C.I.: 1.38-189.71, p = 0.03). . . .acute-phase plasma adrenomedullin concentrations may be the most usefulpredictor of patient prognosis in the setting of AMI, out of the 7 typesof cardiovascular peptides involved in neurohumoral activation. Plasmaadrenomedullin concentrations increased in the acute phase of myocardialinfarction in proportion with clinical severity suggesting thatadrenomedullin may play an important role in the pathophysiology ofmyocardial infarction. Diagnosis of traumatic brain Adrenomedullinconcentration Acta Neurochir Suppl. injury (TBI) in children CSF. wasmarkedly elevated in CSF 2000; 76: 419-21 of children following TBIversus control (mean level 10.65 vs 1.51 fmol/ml, p = 0.006). All 36case samples had an adrenomedullin concentration above the median valuefor the controls (1.52 fmol/ml). Detection of pressure- PlasmaAdrenomedullin- J Card Fail. 2004 overloaded (PO) heart failure mature(VO-HF: +59%, PO-HF: Aug; 10(4): 321-7. (HF) and volume-overloaded +65%,P < .05) and Clin Sci (Lond). 2002 (VO)-HF. Adrenomedullin-glycine (VO-Jun; 102(6): 669-77. HF: +43%, PO-HF: +50%, Heart. 2002 Mar; 87(3):242-6 P < 0.05) were similarly higher in the 2 HF groups than in thecontrol group. Differential diagnosis of Significance 1.2E−4 Proc NatlAcad Sci USA. 2001 Squamous Cell Lung Carcinoma Nov 20; 98(24): 13790-5.VS Adenocarcinoma and/or Carcinoid

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: cAMP biosynthesis; cell-cellsignaling; circulation; pregnancy; progesterone biosynthesis; responseto wounding; signal transduction, which are annotation(s) related toBiological Process; receptor binding, which are annotation(s) related toMolecular Function; and extracellular space; soluble fraction, which areannotation(s) related to Cellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

Cluster F05068 can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of FIG. 27 refer to weightedexpression of ESTs in each category, as “parts per million” (ratio ofthe expression of ESTs for a particular cluster to the expression of allESTs in that category, according to parts per million).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 27 and Table 183. This cluster is overexpressed (atleast at a minimum level) in the following pathological conditions:uterine malignancies.

TABLE 183 Normal tissue distribution Name of Tissue Number brain 31ovary 0 bladder 164 lung 52 pancreas 30 liver 0 general 66 Thyroid 0skin 281 uterus 13 colon 64 kidney 50 lymph nodes 0 breast 86 head andneck 0 stomach 0 epithelial 71 bone 253

TABLE 184 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 brain 5.5e−01 7.1e−01 2.3e−03 1.7 9.9e−02 0.9ovary 3.8e−01 2.6e−01 3.2e−01 2.4 1.6e−01 2.5 bladder 7.6e−01 8.0e−019.4e−01 0.5 9.9e−01 0.4 lung 6.8e−01 5.0e−01 8.5e−01 0.7 3.8e−01 1.0pancreas 4.7e−01 2.8e−01 7.0e−01 0.9 1.0e−01 1.4 liver 1.8e−01 1.3e−012.3e−01 4.3 2.4e−01 2.6 general 3.8e−01 2.7e−01 8.3e−01 0.8 8.8e−01 0.8Thyroid 2.9e−01 2.9e−01 6.8e−01 1.7 6.8e−01 1.7 skin 7.2e−01 6.3e−019.6e−01 0.3 1.0e+00 0.1 uterus 8.7e−02 2.2e−01 2.0e−03 3.2 2.2e−02 2.2colon 6.8e−01 6.7e−01 9.7e−01 0.5 9.6e−01 0.6 kidney 3.4e−01 3.5e−016.1e−02 1.8 1.0e−02 2.1 lymph nodes N/A 3.4e−01 N/A N/A N/A N/A breast7.8e−01 6.3e−01 9.1e−01 0.6 8.9e−01 0.7 head and neck 2.1e−01 1.1e−01N/A N/A 3.2e−01 2.3 stomach 3.3e−01 2.6e−01 N/A N/A 4.0e−01 1.8epithelial 1.2e−01 3.9e−02 7.7e−01 0.7 5.8e−01 0.9 bone 7.5e−01 8.8e−011.0e+00 0.1 1.0e+00 0.3

As noted above, cluster F05068 features 4 transcript(s), which werelisted in Table 178 above. These transcript(s) encode for protein(s)which are variant(s) of protein ADM precursor. A description of eachvariant protein according to the present invention is now provided.

Variant protein F05068_P6 (SEQ ID NO:193) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) F05068_T9 (SEQ ID NO:192).An alignment is given to the known protein (ADM precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between F05068_P6 (SEQ ID NO:193) and ADML_HUMAN(SEQ ID NO:413):

A. An isolated chimeric polypeptide as set forth in F05068_P6 (SEQ IDNO:193), comprising a first amino acid sequence being at least 90%homologous toMKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPEDS corresponding to amino acids 1-83 of ADML_HUMAN (SEQ IDNO:413), which also corresponds to amino acids 1-83 of F05068_P6 (SEQ IDNO:193), and a second amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence CLSSPSPRPQQSGCRPHPSQALPPEHEQLPGPPELWLPLRDVHGAEAGTPDLPVHR (SEQID NO: 490) corresponding to amino acids 84-139 of F05068_P6 (SEQ IDNO:193), wherein said first amino acid sequence and second amino acidsequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of F05068_P6(SEQ ID NO:193), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceCLSSPSPRPQQSGCRPHPSQALPPEHEQLPGPPELWLPLRDVHGAEAGTPDLPVHR (SEQ ID NO:490) of F05068_P6 (SEQ ID NO:193).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein F05068_P6 (SEQ ID NO:193) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table185, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein F05068_P6 (SEQ ID NO:193) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 185 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 V -> F 10 Y -> C 50 S -> R 118 L ->

The phosphorylation sites of variant protein F05068_P6 (SEQ ID NO:193),as compared to the known protein, are described in Table 186 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 186 Phosphorylation site(s) Position(s) on known amino acidPresent in Position(s) on sequence variant protein? variant protein 41Yes 41 146 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 187:

TABLE 187 InterPro domain(s) Domain description Analysis typePosition(s) on protein Adrenomedullin FPrintScan 2-22, 30-46, 49-67Adrenomedullin HMMPfam 21-139

Variant protein F05068_P6 (SEQ ID NO:193) is encoded by the followingtranscript(s): F05068_T9 (SEQ ID NO:192), for which the coding portionstarts at position 267 and ends at position 683. The transcript also hasthe following SNPs as listed in Table 188 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein F05068_P6 (SEQ IDNO:193) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 188 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 26, 206, 960, 1163 T -> 132, 177, 164, 619, 1338 G ->245, 1073 C -> 259, 741, 760, 960. 1151, 1035, 1229 G -> T 276, 1071 A-> G 295, 1434, 1452 A -> C 317, 1452 C -> G 416, 760, 1035, 1151 G -> C443, 904, 1461 C -> A 741, 1071 -> C 909 T -> G 1052, 1338, 1196 T -> C1196, 1549

Variant protein F05068_P9 (SEQ ID NO:194) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) F05068_T6 (SEQ ID NO:189)and F05068_(—)17 (SEQ ID NO:190). An alignment is given to the knownprotein (ADM precursor) in the alignment table on the attached CD-ROM. Abrief description of the relationship of the variant protein accordingto the present invention to each such aligned protein is as follows:

1. Comparison Report Between F05068_P9 (SEQ ID NO:194) and ADML_HUMAN(SEQ ID NO:413):

A. An isolated chimeric polypeptide as set forth in F05068_P9 (SEQ IDNO:194), comprising a amino acid sequence being at least 90% homologousto MKLVSVALMYLGSLAFLGADTARLDVASEFRKK corresponding to amino acids 1-33of ADML_HUMAN (SEQ ID NO:413), which also corresponds to amino acids1-33 of F05068_P9 (SEQ ID NO:194).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein F05068_P9 (SEQ ID NO:194) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table189, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein F05068_P9 (SEQ ID NO:194) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 189 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 V -> F 10 Y -> C

The phosphorylation sites of variant protein F05068_P9 (SEQ ID NO:194),as compared to the known protein, are described in Table 190 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 190 Phosphorylation site(s) Position(s) on known amino acidPresent in Position(s) on sequence variant protein? variant protein 41No 146 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 191:

TABLE 191 InterPro domain(s) Domain description Analysis typePosition(s) on protein Adrenomedullin FPrintScan 2-22, 30-33

Variant protein F05068_P9 (SEQ ID NO:194) is encoded by the followingtranscript(s): F05068_T6 (SEQ ID NO:189) and F05068_T7 (SEQ ID NO:190),for which the coding portion starts at position 267 and ends at position365. The transcript also has the following SNPs as listed in Table 192(given according to their position on the nucleotide sequence, with thealternative nucleic acid listed; the presence of known SNPs in variantprotein F05068_P9 (SEQ ID NO:194) sequence provides support for thededuced sequence of this variant protein according to the presentinvention).

TABLE 192 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 26, 206, 1079, 1282 T -> 132, 164, 177, 738, 1457 G ->245, 1192 C -> 259, 860, 879, 1079, 1270, 1190, 1154, 1348 G -> T 276 A-> G 295, 1553, 1571 A -> C 317, 1571 C -> G 566, 879, 1154, 1270 G -> C593, 1023, 1580 C -> A 860, 1190 -> C 1028 T -> G 1171, 1315, 1457 T ->C 1315, 1668

The coding portion of transcript F05068_T7 (SEQ ID NO:190) codingportion starts at position 267 and ends at position 365. The transcriptalso has the following SNPs as listed in Table 193 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein F05068_P9(SEQ ID NO:194) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 193 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 26, 206, 933, 1136 T -> 132, 164, 177, 592, 1311 G ->245, 1046 C -> 259, 714, 733, 933, 1008, 1124, 1202, 1044 G -> T 276 A-> G 295, 1407, 1425 A -> C 317, 1425 C -> G 420, 733, 1008, 1124 G -> C447, 877, 1434 C -> A 714, 1044 -> C 882 T -> G 1025, 1169, 1311 T -> C1169, 1522

Variant protein F05068_P10 (SEQ ID NO:195) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) F05068_T8 (SEQ ID NO:191).An alignment is given to the known protein (ADM precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between F05068_P10 (SEQ ID NO:195) and ADML_HUMAN(SEQ ID NO:413):

A. An isolated chimeric polypeptide as set forth in F05068_P110 (SEQ IDNO:195), comprising a first amino acid sequence being at least 90%homologous toMKLVSVALMYLGSLAFLGADTARLDVASEFRKKWNKWALSRGKRELRMSSSYPTGLADVKAGPAQTLIRPQDMKGASRSPED corresponding to amino acids 1-82 of ADML_HUMAN (SEQ IDNO:413), which also corresponds to amino acids 1-82 of F05068_P10 (SEQID NO:195), and an amino acid R, wherein said first amino acid sequenceand said amino acid are contiguous and in a sequential order.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein F05068_P10 (SEQ ID NO:195) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table194, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein F05068_P10 (SEQ ID NO:195) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 194 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 4 V -> F 10 Y -> C 50 S -> R

The phosphorylation sites of variant protein F05068_P10 (SEQ ID NO:195),as compared to the known protein, are described in Table 195 (givenaccording to their position(s) on the amino acid sequence in the firstcolumn; the second column indicates whether the phosphorylation site ispresent in the variant protein; and the last column indicates whetherthe position is different on the variant protein).

TABLE 195 Phosphorylation site(s) Position(s) on known amino acidPresent in Position(s) on sequence variant protein? variant protein 41Yes 41 146 No

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 196:

TABLE 196 InterPro domain(s) Domain description Analysis typePosition(s) on protein Adrenomedullin FPrintScan 2-22, 30-46, 49-67

Variant protein F05068_P10 (SEQ ID NO:195) is encoded by the followingtranscript(s): F05068_T8 (SEQ ID NO:191), for which the coding portionstarts at position 267 and ends at position 515. The transcript also hasthe following SNPs as listed in Table 197 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein F05068_P10 (SEQ IDNO:195) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 197 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 26, 206, 1162, 1365 T -> 132, 164, 177, 821, 1540 G ->245, 1275 C -> 259, 943, 962, 1162, 1237, 1273, 1431, 1353 G -> T 276 A-> G 295, 1636, 1654 A -> C 317, 1654 C -> G 416, 589, 962, 1237, 1353 G-> C 443 C -> A 943, 1273 G -> C 1106, 1663 -> C 1111 T -> G 1254, 1398,1540 T -> C 1398, 1751

As noted above, cluster F05068 features 15 segment(s), which were listedin Table 179 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segments 3, 5, 9, and 13 according to the present invention is nowprovided.

Segment cluster F05068_N5 (SEQ ID NO:199) according to the presentinvention is supported by 19 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): F05068_T6 (SEQ ID NO:189). Table 198 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 198 Segment location on transcripts Segment Segment Transcriptname starting position ending position F05068_T6 (SEQ ID NO: 189) 369514

Segment cluster F05068_N9 (SEQ ID NO:203) according to the presentinvention is supported by 16 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): F05068_T8 (SEQ ID NO:191). Table 199 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 199 Segment location on transcripts Segment Segment Transcriptname starting position ending position F05068_T8 (SEQ ID NO: 191) 515716

Segment cluster F05068_N13 (SEQ ID NO:207) according to the presentinvention is supported by 180 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): F05068_T6 (SEQ ID NO:189), F05068_T7 (SEQ IDNO:190), F05068_T8 (SEQ ID NO:191) and F05068_T9 (SEQ ID NO:192). Table200 below describes the starting and ending position of this segment oneach transcript.

TABLE 200 Segment location on transcripts Segment Segment Transcriptname starting position ending position F05068_T6 (SEQ ID NO: 189) 749909 F05068_T7 (SEQ ID NO: 190) 603 763 F05068_T8 (SEQ ID NO: 191) 832992 F05068_T9 (SEQ ID NO: 192) 630 790

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster F05068_N3 (SEQ ID NO:197) according to the presentinvention is supported by 200 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): F05068_T6 (SEQ ID NO:189), F05068_T7 (SEQ IDNO:190), F05068_T8 (SEQ ID NO:191) and F05068_T9 (SEQ ID NO:192). Table201 below describes the starting and ending position of this segment oneach transcript.

TABLE 201 Segment location on transcripts Segment Segment Transcriptname starting position ending position F05068_T6 (SEQ ID NO: 189) 246364 F05068_T7 (SEQ ID NO: 190) 246 364 F05068_T8 (SEQ ID NO: 191) 246364 F05068_T9 (SEQ ID NO: 192) 246 364

FIG. 28 shows the structure of the F05068 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

Expression of Homo sapiens Adrenomedullin (ADM) F05068 Transcripts whichare Detectable by Amplicon as Depicted in Sequence Name F05068 seg3-5(SEQ ID NO: 414) in Different Normal Tissues

Expression of Homo sapiens adrenomedullin (ADM) transcripts detectableby or according to F05068 seg3-5 amplicon (SEQ ID NO: 414) and primers:F05068 seg3-5F (SEQ ID NO: 415) and F05068 seg3-5R (SEQ ID NO: 416) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes—RPL19 (GenBank Accession No. NM_(—)000981 (SEQ IDNO:369); RPL19 (SEQ ID NO:368) amplicon), TATA box (GenBank AccessionNo. NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon),Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) and SDHA (GenBank AccessionNo. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ IDNO:365)) was measured similarly. For each RT sample, the expression ofthe above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the lungsamples (Sample Nos. 15-17 Table 5), to obtain a value of relativeexpression of each sample relative to median of the lung samples. FIG.29 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068 seg3-5 (SEQ ID NO: 414) in different normal tissues.

Forward primer F05068 seg3-5F (SEQ ID NO: 415): TGGTTTCCGTCGCCCTGATGReverse primer F05068 seg3-5R (SEQ ID NO: 416): CTTCGGGACCAACGGTCAGTTCAmplicon F05068 seg3-5 (SEQ ID NO: 414):TGGTTTCCGTCGCCCTGATGTACCTGGGTTCGCTCGCCTTCCTAGGCGCTGACACCGCTCGGTTGGATGTCGCGTCGGAGTTTCGAAAGAAGTGAGTCCGGGCAGCGCCTTCCCCCTTGCTGGTACCTGGCAGGCAAGGGGAACTGACCG TTGGTCCCGAAGExpression of Homo sapiens Adrenomedullin (ADM) F05068 Transcripts whichare Detectable by Amplicon as Depicted in Sequence Name F05068 seg9 (SEQID NO: 417) in Normal and Cancerous Lung Tissues

Expression of Homo sapiens adrenomedullin (ADM) transcripts detectableby or according to seg9, F05068 seg9 amplicon (SEQ ID NO: 417) andprimers F05068 seg9F (SEQ ID NO: 418) and F05068 seg9R (SEQ ID NO: 419)was measured by real time PCR. In parallel the expression of fourhousekeeping genes —PBGD (GenBank Accession No. BC019323 (SEQ IDNO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), Ubiquitin (GenBank Accession No. BC000449 (SEQ IDNO:366); amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) and SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), was measured similarly. For each RT sample, the expressionof the above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (Sample Nos. 47-50, 90-93, 96-99, Table 3).Then the reciprocal of this ratio was calculated, to obtain a value offold down-regulation for each sample relative to median of the normal PMsamples.

FIG. 30 is a histogram showing down regulation of the above-indicatedHomo sapiens adrenomedullin (ADM) transcripts in cancerous lung samplesrelative to the normal samples (seg9).

As is evident from FIG. 30, the expression of Homo sapiensadrenomedullin (ADM) transcripts detectable by the above amplicon incancer samples was lower than in the non-cancerous samples (Sample Nos.46-50, 90-93, 96-99 Table 3). Notably down regulation of at least 5 foldwas found in 4 out of 8 small cell carcinoma samples.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: F05068 seg9F (SEQ ID NO: 418) forward primer; andF05068 seg9R (SEQ ID NO: 419) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: F05068 seg9 (SEQ IDNO: 417).

Forward primer F05068 seg9F (SEQ ID NO: 418): ACGGGAGGGAAGGAAGGTGReverse primer F05068 seg9R (SEQ ID NO: 419): CAGAGGGAGCTGGAAAGTGCAmplicon F05068 seg9 (SEQ ID NO: 417):ACGGGAGGGAAGGAAGGTGTGCGGGAGGAGTTCTCTGTCTCCACTCCCCTGGCCCGGGGGATCGTCGGGGCTGGACCGCAGCTCAGATGGCGCGAGCAGT TTCCAGCTCCCTCTGExpression of Homo sapiens Adrenomedullin (ADM) F05068 Transcripts whichare Detectable by Amplicon as Depicted in Sequence Name F05068_seg9 (SEQID NO: 417) in Different Normal Tissues

Expression of Homo sapiens adrenomedullin (ADM) transcripts detectableby or according to seg9-F05068_seg9 (SEQ ID NO: 417) amplicon andprimers F05068_seg9F (SEQ ID NO: 418) and F05068_seg9R (SEQ ID NO: 419)was measured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the lung samples (samplenumbers 15, 16 and 17, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the lung samples. FIG.31 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068_seg9 (SEQ ID NO: 417) in different normal tissues.

Forward primer (F05068_seg9F (SEQ ID NO: 418)): ACGGGAGGGAAGGAAGGTGReverse primer (F05068_seg9R (SEQ ID NO: 419)): CAGAGGGAGCTGGAAAGTGCAmplicon (F05068_seg9 (SEQ ID NO: 417)):ACGGGAGGGAAGGAAGGTGTGCGGGAGGAGTTCTCTGTCTCCACTCCCCTGGCCCGGGGGATCGTCGGGGCTGGACCGCAGCTCAGATGGCGCGAGCAGT TTCCAGCTCCCTCTGExpression of Homo sapiens Adrenomedullin (ADM) F05068 Transcripts whichare Detectable by Amplicon as Depicted in Sequence Name F05068_seg13_WT(SEQ ID NO:420) in Different Normal Tissues

Expression of Homo sapiens adrenomedullin (ADM) transcripts detectableby or according to seg13_WT—F05068_seg13_WT (SEQ ID NO:420) amplicon andprimers F05068-seg13F_WT (SEQ ID NO:421) and F05068_seg13R_WT (SEQ IDNO:422) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the lung samples (samplenumbers 15, 16 and 17, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the lung samples. FIG.32 shows expression of Homo sapiens adrenomedullin (ADM) F05068transcripts which are detectable by amplicon as depicted in sequencename F05068_seg13_WT (SEQ ID NO:420) in different normal tissues.

Forward Primer (F05068_seg13F_WT (SEQ ID NO:421)): TGCACGGTGCAGAAGCTGReverse Primer (F05068_seg13R_WT (SEQ ID NO:422)): CGGCCGTAGCCCTGGAmplicon (F05068_seg13_WT (SEQ ID NO:420)):TGCACGGTGCAGAAGCTGGCACACCAGATCTACCAGTTCACAGATAAGGACAAGGACAACGTCGCCCCCAGGAGCAAGATCAGCCCCCAGGGCTACGGCC G

Expression of Homo sapiens adrenomedullin (ADM) F05068 transcripts whichare detectable by amplicon as depicted in sequence name F05068 seg3-5(SEQ ID NO: 414) in normal and cancerous Lung tissues

Expression of Homo sapiens adrenomedullin (ADM) transcripts detectableby or according to seg3-5, F05068 seg3-5 (SEQ ID NO: 414) amplicon andprimers F05068 seg3-5F (SEQ ID NO: 415) and F05068 seg3-5R (SEQ ID NO:416) was measured by real time PCR. In parallel the expression of fourhousekeeping genes —PBGD (GenBank Accession No. BC019323 (SEQ IDNO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), Ubiquitin (GenBank Accession No. BC000449 (SEQ IDNO:366); amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) and SDHA (GenBankAccession No. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQID NO:365)), was measured similarly. For each RT sample, the expressionof the above amplicon was normalized to the geometric mean of thequantities of the housekeeping genes. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalpost-mortem (PM) samples (Sample Nos. 47-50, 90-93, 96-99, Table 3).

FIG. 33 is a histogram showing over expression of the above-indicatedHomo sapiens adrenomedullin (ADM) transcripts in cancerous lung samplesrelative to the normal samples.

As is evident from FIG. 33, the expression of Homo sapiensadrenomedullin (ADM) transcripts detectable by the above amplicon washigher in several cancer samples than in the non-cancerous samples(Sample Nos. 46-50, 90-93, 96-99 Table 3). Notably over expression of atleast 5 fold was found in 6 out of 35 non-small cells carcinoma samples.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: F05068 seg seg3-5F (SEQ ID NO: 415) forwardprimer; and F05068 seg seg3-5R (SEQ ID NO: 416) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: F05068 seg3-5 (SEQ IDNO: 414).

Forward primer F05068 seg3-5F (SEQ ID NO: 415): TGGTTTCCGTCGCCCTGATGReverse primer F05068 seg3-5R (SEQ ID NO: 416): CTTCGGGACCAACGGTCAGTTCAmplicon F05068 seg3-5 (SEQ ID NO: 414):TGGTTTCCGTCGCCCTGATGTACCTGGGTTCGCTCGCCTTCCTAGGCGCTGACACCGCTCGGTTGGATGTCGCGTCGGAGTTTCGAAAGAAGTGAGTCCGGGCAGCGCCTTCCCCCTTGCTGGTACCTGGCAGGCAAGGGGAACTGACCG TTGGTCCCGAAG

Homo sapiens adrenomedullin (ADM) F05068 transcripts which aredetectable by amplicon as depicted in sequence name F05068_seg13_WT (SEQID NO:420) and primers F05068_seg13_WT-F (SEQ ID NO: 421) andF05068_seg13_WT-R (SEQ ID NO: 422) did not show any differentialexpression in one experiment carried out with lung cancer panel.

Homo sapiens adrenomedullin (ADM) F05068 transcripts which aredetectable by amplicon as depicted in sequence name F05068_seg9 (SEQ IDNO: 417) and primers F05068_seg9-F (SEQ ID NO: 418) and F05068_seg9-R(SEQ ID NO: 419) did not show any differential expression in oneexperiment carried out with breast cancer panel.

Description for Cluster HUMIL10

Cluster HUMIL10 features 4 transcript(s) and 15 segment(s) of interest,the names for which are given in Tables 202 and 203, respectively. Theselected protein variants are given in table 204.

TABLE 202 Transcripts of interest Transcript Name HUMIL10_T5 (SEQ ID NO:211) HUMIL10_T6 (SEQ ID NO: 212) HUMIL10_T8 (SEQ ID NO: 213) HUMIL10_T10(SEQ ID NO: 214)

TABLE 203 Segments of interest Segment Name HUMIL10_N0 (SEQ ID NO: 220)HUMIL10_N5 (SEQ ID NO: 223) HUMIL10_N6 (SEQ ID NO: 224) HUMIL10_N10 (SEQID NO: 225) HUMIL10_N14 (SEQ ID NO: 227) HUMIL10_N16 (SEQ ID NO: 229)HUMIL10_N19 (SEQ ID NO: 232) HUMIL10_N1 (SEQ ID NO: 221) HUMIL10_N3 (SEQID NO: 222) HUMIL10_N11 (SEQ ID NO: 226) HUMIL10_N15 (SEQ ID NO: 228)HUMIL10_N17 (SEQ ID NO: 230) HUMIL10_N18 (SEQ ID NO: 231) HUMIL10_N20(SEQ ID NO: 233) HUMIL10_N21 (SEQ ID NO: 234)

TABLE 204 Proteins of interest Protein Name Corresponding Transcript(s)HUMIL10_P6 (SEQ ID NO: 215) HUMIL10_T6 (SEQ ID NO: 212) HUMIL10_P9 (SEQID NO: 216) HUMIL10_T10 (SEQ ID NO: 214) HUMIL10_P10 (SEQ ID NO: 217)HUMIL10_T5 (SEQ ID NO: 211) HUMIL10_P12 (SEQ ID NO: 218) HUMIL10_T8 (SEQID NO: 213) HUMIL10_P13 (SEQ ID NO: 219) HUMIL10_T10 (SEQ ID NO: 214)

These sequences are variants of the known protein Interleukin-10precursor (SwissProt accession identifier IL10_HUMAN (SEQ ID NO:423);known also according to the synonyms IL-10; Cytokine synthesisinhibitory factor; CSIF), referred to herein as the previously knownprotein.

Protein Interleukin-10 precursor is known or believed to have thefollowing function(s): Inhibits the synthesis of a number of cytokines,including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activatedmacrophages and by helper T cells. The sequence for proteinInterleukin-10 precursor is given at the end of the application, as“Interleukin-10 precursor amino acid sequence”. Known polymorphisms forthis sequence are as shown in Table 205.

TABLE 205 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 15 G -> R (in CD; decreases secretionthereby reducing the anti-inflammatory effect). /FTId = VAR_015883

Protein Interleukin-10 precursor localization is believed to beSecreted.

The previously known protein also has the following indication(s) and/orpotential therapeutic use(s): Inflammation, general; Inflammatory boweldisease; Pain, neuropathic. It has been investigated forclinical/therapeutic use in humans, for example as a target for anantibody or small molecule, and/or as a direct therapeutic; availableinformation related to these investigations is as follows. Potentialpharmaceutically related or therapeutically related activity oractivities of the previously known protein are as follows: Interleukin10 agonist. A therapeutic role for a protein represented by the clusterhas been predicted. The cluster was assigned this field because therewas information in the drug database or the public databases (e.g.,described herein above) that this protein, or part thereof, is used orcan be used for a potential therapeutic indication: Analgesic, other;Anti-inflammatory; Cytokine; GI inflammatory/bowel disorders;Recombinant interleukin.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: anti-apoptosis; B-celldifferentiation; B-cell proliferation; cell-cell signaling; cytoplasmicsequestering of NF-kappaB; hemopoiesis; immune cell chemotaxis; negativeregulation of interferon-alpha biosynthesis; negative regulation ofinterferon-gamma biosynthesis; negative regulation of MHC class IIbiosynthesis; negative regulation of nitric oxide biosynthesis; negativeregulation of T-cell proliferation; regulation of isotype switching;T-helper 2 type immune response, which are annotation(s) related toBiological Process; interleukin-10 receptor binding, which areannotation(s) related to Molecular Function; and extracellular region,which are annotation(s) related to Cellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

IL-10 is a cytokine that has pleiotropic effects in immunoregulation andinflammation. It down-regulates the expression of Th1 cytokines, MHCclass II Ags, and co-stimulatory molecules on macrophages. It alsoenhances B cell survival, proliferation, and antibody production.Therefore any condition featuring an imbalance between Th1 to Th2 isrelevant (such as Crohn's disease for example, although of course manyother such diseases could be included).

TABLE 206 Dx field Explanation Ref IL10 alone or the ratio of IL-10 TheIL-10/IL-6 ratio was Hepatogastroenterology. 2005 to IL6 can serve asmarker for significantly lower in patients July-August; 52(64): 990-4.acute pancreatitis severity. with severe acute pancreatitis, Gut. 1999December; 45(6): 895-9. suggesting that a Pancreas. 1999 May; 18(4):371-7. proinflammatory response was predominant in these patientsDifferential diagnosis of Both the frequency and the Ann Rheum Dis 1998;57: 691-693 psoriatic arthritis (PsA) to concentrations of cytokines(November) rheumatoid arthritis (RA) and (IL10 among others) wereosteoarthritis (OA), in synovial lower in PsA SFs than in RA fluid. SFs,while OA SFs generally lacked any detectable T cell cytokinesaltogether. Differentiation between levels of the anti-inflammatorysystemic sclerosis (SSc) IL10 were higher in SSc-ILD interstitial lungdisease to than in controls. idiopathic usual interstitial pneumonia inbronchoalveolar lavage fluid. Might be used in combination with IL-12and/or MCP-1 Detection and outcome IL-6, TNFalpha and IL-10 CardiovascRes. 2005 May prediction of cardiovascular levels have been shown to 1;66(2): 265-75. Epub 2005 Jan. disease in people >65. alone or predictcardiovascular 28. in combination with IL6 and or outcomes. TNF alpha

As noted above, cluster HUMIL10 features 4 transcript(s), which werelisted in Table 202 above. These transcript(s) encode for protein(s)which are variant(s) of protein Interleukin-10 precursor. A descriptionof each variant protein according to the present invention is nowprovided.

Variant protein HUMIL10_P6 (SEQ ID NO:215) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMIL10_T6 (SEQ ID NO:212).An alignment is given to the known protein (Interleukin-10 precursor) inthe alignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMIL10_P6 (SEQ ID NO:215) and IL10_HUMAN(SEQ ID NO:423):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P6 (SEQ IDNO:215), comprising an amino acid sequence being at least 90% homologoustoMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding to amino acids 86-178 of IL10_HUMAN(SEQ ID NO:423), which also corresponds to amino acids 1-93 ofHUMIL10_P6 (SEQ ID NO:215).

2. Comparison Report Between HUMIL10_P6 (SEQ ID NO:215) and Q6FGS9_HUMAN(SEQ ID NO: 545):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P6 (SEQ IDNO:215), comprising a first amino acid sequence being at least 90%homologous to MIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRC corresponding toamino acids 86-126 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 1-41 of HUMIL10_P6 (SEQ ID NO:215), abridging amino acid H corresponding to amino acid 42 of HUMIL10_P6 (SEQID NO:215), and a second amino acid sequence being at least 90%homologous to RFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRNcorresponding to amino acids 128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545),which also corresponds to amino acids 43-93 of HUMIL10_P6 (SEQ IDNO:215), wherein said first amino acid sequence, bridging amino acid andsecond amino acid sequence are contiguous and in a sequential order.

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellularly.

Variant protein HUMIL10_P6 (SEQ ID NO:215) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table207, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMIL10_P6 (SEQ ID NO:215) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 207 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 26 S ->

The glycosylation sites of variant protein HUMIL10_P6 (SEQ ID NO:215),as compared to the known protein Interleukin-10 precursor, are describedin Table 208 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 208 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 134Yes 49

Variant protein HUMIL10_P6 (SEQ ID NO:215) is encoded by the followingtranscript(s): HUMIL10_T6 (SEQ ID NO:212), for which the coding portionstarts at position 171 and ends at position 449. The transcript also hasthe following SNPs as listed in Table 209 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HUMIL10_P6 (SEQ IDNO:215) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 209 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> 247 C -> T 260, 569, 1213 T -> C 488 A -> G 643, 904, 1404A -> 772 A -> T 797 G -> A 970, 1067

Variant protein HUMIL10_P9 (SEQ ID NO:216) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMIL10_T10 (SEQ ID NO:214).An alignment is given to the known protein (Interleukin-10 precursor) inthe alignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMIL10_P9 (SEQ ID NO:216) and IL10_HUMAN(SEQ ID NO:423):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P9 (SEQ IDNO:216), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 584)corresponding to amino acids 1-28 of HUMIL10_P9 (SEQ ID NO:216), and asecond amino acid sequence being at least 90% homologous toHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 127-178 of IL10_HUMAN (SEQ ID NO:423), which alsocorresponds to amino acids 29-80 of HUMIL10_P9 (SEQ ID NO:216), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P9 (SEQ IDNO:216), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 584) of HUMIL10_P9(SEQ ID NO:216).

2. Comparison Report Between HUMIL10_P9 (SEQ ID NO:216) and Q71UZ1_HUMAN(SEQ ID NO: 542):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P9 (SEQ IDNO:216), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MMPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 584)corresponding to amino acids 1-28 of HUMIL10_P9 (SEQ ID NO:216), and asecond amino acid sequence being at least 90% homologous toHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 109-160 of Q71UZ1_HUMAN (SEQ ID NO: 542), which alsocorresponds to amino acids 29-80 of HUMIL10_P9 (SEQ ID NO:216), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

3. Comparison Report Between HUMIL10_P9 (SEQ ID NO:216) and Q6FGS9_HUMAN(SEQ ID NO: 545):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P9 (SEQ IDNO:216), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MMPPACPLSVMDMELEARITNTFSFLPQH (SEQ ID NO: 585)corresponding to amino acids 1-29 of HUMIL10_P9 (SEQ ID NO:216), and asecond amino acid sequence being at least 90% homologous toRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 30-80 of HUMIL10_P9 (SEQ ID NO:216), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P9 (SEQ IDNO:216), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MMPPACPLSVMDMELEARITNTFSFLPQH (SEQ ID NO: 585) of HUMIL10_P9(SEQ ID NO:216).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellularly.

The glycosylation sites of variant protein HUMIL10_P9 (SEQ ID NO:216),as compared to the known protein Interleukin-10 precursor, are describedin Table 210 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 210 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 134Yes 36

Variant protein HUMIL10_P9 (SEQ ID NO:216) is encoded by the followingtranscript(s): HUMIL10_T10 (SEQ ID NO:214), for which the coding portionstarts at position 182 and ends at position 421. The transcript also hasthe following SNPs as listed in Table 211 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HUMIL10_P9 (SEQ IDNO:216) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 211 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence T -> G  95 G -> A 140, 942, 1039 A -> G 154, 615, 876, 1376 T-> C 208, 460 C -> T 541, 1185 A -> 744 A -> T 769

Variant protein HUMIL10_P10 (SEQ ID NO:217) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMIL10_T5 (SEQ ID NO:211).An alignment is given to the known protein (Interleukin-10 precursor) inthe alignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMIL10_P10 (SEQ ID NO:217) and IL10_HUMAN(SEQ ID NO:423):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P10 (SEQ IDNO:217), comprising a first amino acid sequence being at least 90%homologous to MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRcorresponding to amino acids 1-50 of IL10_HUMAN (SEQ ID NO:423), whichalso corresponds to amino acids 1-50 of HUMIL10_P10 (SEQ ID NO:217), anda second amino acid sequence being at least 90% homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 56-178 of IL10_HUMAN (SEQ ID NO:423), whichalso corresponds to amino acids 51-173 of HUMIL10_P10 (SEQ ID NO:217),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHUMIL10_P10 (SEQ ID NO:217), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise RQ, having a structure as follows: asequence starting from any of amino acid numbers 50−x to 50; and endingat any of amino acid numbers 51+((n−2)−x), in which x varies from 0 ton−2.

2. Comparison Report Between HUMIL10_P10 (SEQ ID NO:217) andQ6FGS9_HUMAN (SEQ ID NO:545)

A. An isolated chimeric polypeptide as set forth in HUMIL10_P10 (SEQ IDNO:217), comprising a first amino acid sequence being at least 90%homologous to MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRcorresponding to amino acids 1-50 of Q6FGS9_HUMAN (SEQ ID NO: 545),which also corresponds to amino acids 1-50 of HUMIL10_P10 (SEQ IDNO:217), a second amino acid sequence being at least 90% homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAH NSLGENLKTLRLRLRRCcorresponding to amino acids 56-126 of Q6FGS9_HUMAN (SEQ ID NO: 545),which also corresponds to amino acids 51-121 of HUMIL10_P10 (SEQ IDNO:217), a bridging amino acid H corresponding to amino acid 122 ofHUMIL10_P10 (SEQ ID NO:217), and a third amino acid sequence being atleast 90% homologous toRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 123-173 of HUMIL10_P10 (SEQ ID NO:217),wherein said first amino acid sequence, second amino acid sequence,bridging amino acid and third amino acid sequence are contiguous and ina sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHUMIL10_P10 (SEQ ID NO:217), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise RQ, having a structure as follows: asequence starting from any of amino acid numbers 50−x to 50; and endingat any of amino acid numbers 51+((n−2)−x), in which x varies from 0 ton−2.

3. Comparison Report Between HUMIL10_PLO (SEQ ID NO:217) andQ71UZ1_HUMAN (SEQ ID NO: 542):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P10 (SEQ IDNO:217), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) corresponding toamino acids 1-18 of HUMIL10_P10 (SEQ ID NO:217), a second amino acidsequence being at least 90% homologous toSPGQGTQSENSCTHFPGNLPNMLRDLRDAFSR corresponding to amino acids 1-32 ofQ71UZ1_HUMAN (SEQ ID NO: 542), which also corresponds to amino acids19-50 of HUMIL10_P10 (SEQ ID NO:217), and a third amino acid sequencebeing at least 90% homologous toQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 38-160 of Q71UZ1_HUMAN (SEQ ID NO: 542),which also corresponds to amino acids 51-173 of HUMIL10_P10 (SEQ IDNO:217), wherein said first amino acid sequence, second amino acidsequence and third amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P10 (SEQ IDNO:217), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) of HUMIL10_P10 (SEQ IDNO:217).

C. An isolated chimeric polypeptide encoding for an edge portion ofHUMIL10_P10 (SEQ ID NO:217), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise RQ, having a structure as follows: asequence starting from any of amino acid numbers 50−x to 50; and endingat any of amino acid numbers 51+((n−2)−x), in which x varies from 0 ton−2.

6. Comparison Report Between HUMIL10_PLO (SEQ ID NO:217) andQ6LBF4_HUMAN (SEQ ID NO: 546):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P10 (SEQ IDNO:217), comprising a first amino acid sequence being at least 90%homologous to MHSSALLCCLVLLTGVPASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRcorresponding to amino acids 1-50 of Q6LBF4_HUMAN (SEQ ID NO: 546),which also corresponds to amino acids 1-50 of HUMIL10_P10 (SEQ IDNO:217), and a second amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491)corresponding to amino acids 51-173 of HUMIL10_P10 (SEQ ID NO:217),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMIL10_P10(SEQ ID NO:217), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 491) ofHUMIL10_P10 (SEQ ID NO:217).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMIL10_P10 (SEQ ID NO:217) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table212, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMIL10_P10 (SEQ ID NO:217) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 212 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 106 S ->

The glycosylation sites of variant protein HUMIL10_P10 (SEQ ID NO:217),as compared to the known protein Interleukin-10 precursor, are describedin Table 213 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 213 Glycosylation site(s) Position(s) on known Present inPosition(s) on amino acid sequence variant protein? variant protein 134Yes 129

Variant protein HUMIL10_P10 (SEQ ID NO:217) is encoded by the followingtranscript(s): HUMIL10_T5 (SEQ ID NO:211), for which the coding portionstarts at position 60 and ends at position 578. The transcript also hasthe following SNPs as listed in Table 214 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HUMIL10_P10 (SEQID NO:217) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 214 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> 376 C -> T 389, 698, 1342 T -> C 617 A -> G 772, 1033,1533 A -> 901 A -> T 926 G -> A 1099, 1196

Variant protein HUMIL10_P12 (SEQ ID NO:218) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMIL10_T8 (SEQ ID NO:213).An alignment is given to the known protein (Interleukin-10 precursor) inthe alignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMIL10_P12 (SEQ ID NO:218) and IL10_HUMAN(SEQ ID NO:423):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P12 (SEQ IDNO:218), comprising a first amino acid sequence being at least 90%homologous toMHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRC corresponding toamino acids 1-126 of IL10_HUMAN (SEQ ID NO:423), which also correspondsto amino acids 1-126 of HUMIL10_P12 (SEQ ID NO:218), and a second aminoacid sequence being at least 90% homologous toLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding to amino acids 149-178 ofIL10_HUMAN (SEQ ID NO:423), which also corresponds to amino acids127-156 of HUMIL10_P12 (SEQ ID NO:218), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofHUMIL10_P12 (SEQ ID NO:218), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise CL, having a structure as follows: asequence starting from any of amino acid numbers 126−x to 126; andending at any of amino acid numbers 127+((n−2)−x), in which x variesfrom 0 to n−2.

5. Comparison Report Between HUMIL10_P12 (SEQ ID NO:218) andQ71UZ1_HUMAN (SEQ ID NO: 542):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P12 (SEQ IDNO:218), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) corresponding toamino acids 1-18 of HUMIL10_P12 (SEQ ID NO:218), a second amino acidsequence being at least 90% homologous toSPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRC corresponding to amino acids 1-108of Q71UZ1_HUMAN (SEQ ID NO: 542), which also corresponds to amino acids19-126 of HUMIL10_P12 (SEQ ID NO:218), and a third amino acid sequencebeing at least 90% homologous to LQEKGIYKAMSEFDIFINYIEAYMTMKIRNcorresponding to amino acids 131-160 of Q71UZ1_HUMAN (SEQ ID NO: 542),which also corresponds to amino acids 127-156 of HUMIL10_P12 (SEQ IDNO:218), wherein said first amino acid sequence, second amino acidsequence and third amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P12 (SEQ IDNO:218), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MHSSALLCCLVLLTGVRA (SEQ ID NO: 586) of HUMIL10_P12 (SEQ IDNO:218).

C. An isolated chimeric polypeptide encoding for an edge portion ofHUMIL10_P12 (SEQ ID NO:218), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise CL, having a structure as follows: asequence starting from any of amino acid numbers 126−x to 126; andending at any of amino acid numbers 127+((n−2)−x), in which x variesfrom 0 to n−2.

6. Comparison Report Between HUMIL10_P12 (SEQ ID NO:218) andQ6LBF4_HUMAN (SEQ ID NO: 546):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P12 (SEQ IDNO:218), comprising a first amino acid sequence being at least 90%homologous to MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFcorresponding to amino acids 1-55 of Q6LBF4_HUMAN (SEQ ID NO: 546),which also corresponds to amino acids 1-55 of HUMIL10_P12 (SEQ IDNO:218), and a second amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 492) corresponding to aminoacids 56-156 of HUMIL10_P12 (SEQ ID NO:218), wherein said first aminoacid sequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide as set forth in a tail of HUMIL10_P12 (SEQ IDNO:218), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequenceQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCLQEKGIYKAMSEFDIFINYIEAYMTMKIRN (SEQ ID NO: 492) of HUMIL10_P12 (SEQ IDNO:218)

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is secreted.

Variant protein HUMIL10_P12 (SEQ ID NO:218) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table215, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMIL10_P12 (SEQ ID NO:218) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 215 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 111 S ->

The glycosylation sites of variant protein HUMIL10_P12 (SEQ ID NO:218),as compared to the known protein Interleukin-10 precursor, are describedin Table 216 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 216 Glycosylation site(s) Position(s) on known Present inPosition(s) amino acid sequence variant protein? on variant protein 134No

Variant protein HUMIL10_P12 (SEQ ID NO:218) is encoded by the followingtranscript(s): HUMIL10_T8 (SEQ ID NO:213), for which the coding portionstarts at position 60 and ends at position 527. The transcript also hasthe following SNPs as listed in Table 217 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HUMIL10_P12 (SEQID NO:218) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 217 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> 391 C -> T 404, 647, 1291 T -> C 566 A -> G 721, 982, 1482A -> 850 A -> T 875 G -> A 1048, 1145

Variant protein HUMIL10_P13 (SEQ ID NO:219) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMIL10_T10 (SEQ ID NO:214).An alignment is given to the known protein (Interleukin-10 precursor) inthe alignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between HUMIL10_P13 (SEQ ID NO:219) and IL10_HUMAN(SEQ ID NO:423):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P13 (SEQ IDNO:219), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587)corresponding to amino acids 1-27 of HUMIL10_P13 (SEQ ID NO:219), and asecond amino acid sequence being at least 90% homologous toHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 127-178 of IL10_HUMAN (SEQ ID NO:423), which alsocorresponds to amino acids 28-79 of HUMIL10_P13 (SEQ ID NO:219), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P13 (SEQ IDNO:219), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587) of HUMIL10_P13(SEQ ID NO:219).

2. Comparison Report Between HUMIL10_P13 (SEQ ID NO:219) andQ71UZ1_HUMAN (SEQ ID NO: 542):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P13 (SEQ IDNO:219), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587)corresponding to amino acids 1-27 of HUMIL10_P13 (SEQ ID NO:219), and asecond amino acid sequence being at least 90% homologous toHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 109-160 of Q71UZ1_HUMAN (SEQ ID NO: 542), which alsocorresponds to amino acids 28-79 of HUMIL10_P13 (SEQ ID NO:219), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P13 (SEQ IDNO:219), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MPPACPLSVMDMELEARITNTFSFLPQ (SEQ ID NO: 587) of HUMIL10_P13(SEQ ID NO:219).

5. Comparison Report Between HUMIL10_P13 (SEQ ID NO:219) andQ6FGS9_HUMAN (SEQ ID NO: 545):

A. An isolated chimeric polypeptide as set forth in HUMIL10_P13 (SEQ IDNO:219), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequence MPPACPLSVMDMELEARITNTFSFLPQH (SEQ ID NO: 588)corresponding to amino acids 1-28 of HUMIL10_P13 (SEQ ID NO:219), and asecond amino acid sequence being at least 90% homologous toRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN corresponding toamino acids 128-178 of Q6FGS9_HUMAN (SEQ ID NO: 545), which alsocorresponds to amino acids 29-79 of HUMIL10_P13 (SEQ ID NO:219), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of HUMIL10_P13 (SEQ IDNO:219), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequence MPPACPLSVMDMELEARITNTFSFLPQH (SEQ ID NO: 588) of HUMIL10_P13(SEQ ID NO:219).

The location of the variant protein was determined according to resultsfrom a number of different software programs and analyses, includinganalyses from SignalP and other specialized programs. The variantprotein is intracellular.

The glycosylation sites of variant protein HUMIL10_P13 (SEQ ID NO:219),as compared to the known protein Interleukin-10 precursor, are describedin Table 218 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 218 Glycosylation site(s) Position(s) on known Present inPosition(s) amino acid sequence variant protein? on variant protein 134Yes 35

Variant protein HUMIL10_P13 (SEQ ID NO:219) is encoded by the followingtranscript(s): HUMIL10_T10 (SEQ ID NO:214), for which the coding portionstarts at position 185 and ends at position 421. The transcript also hasthe following SNPs as listed in Table 219 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein HUMIL10_P13 (SEQID NO:219) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 219 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence T -> G  95 G -> A 140, 942, 1039 A -> G 154, 1376, 615, 876 T-> C 208, 460 C -> T 541, 1185 A -> 744 A -> T 769

As noted above, cluster HUMIL10 features 15 segment(s), which werelisted in Table 203 above and for which the sequence(s) are given at theend of the application. These segment(s) are portions of nucleic acidsequence(s) which are described herein separately because they are ofparticular interest. A description of each segment according to thepresent invention is now provided.

Segment cluster HUMIL10_N0 (SEQ ID NO:220) according to the presentinvention is supported by 37 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T5 (SEQ ID NO:211) and HUMIL10_T8 (SEQID NO:213). Table 220 below describes the starting and ending positionof this segment on each transcript.

TABLE 220 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T5 (SEQ ID NO: 211) 1 209HUMIL10_T8 (SEQ ID NO: 213) 1 209

Segment cluster HUMIL10_N5 (SEQ ID NO:223) according to the presentinvention is supported by 4 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T6 (SEQ ID NO:212). Table 221 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 221 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T6 (SEQ ID NO: 212) 1 140

Segment cluster HUMIL10 N6 (SEQ ID NO:224) according to the presentinvention is supported by 53 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T5 (SEQ ID NO:211), HUMIL10_T6 (SEQ IDNO:212) and HUMIL10_T8 (SEQ ID NO:213). Table 222 below describes thestarting and ending position of this segment on each transcript.

TABLE 222 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T5 (SEQ ID NO: 211) 270422 HUMIL10_T6 (SEQ ID NO: 212) 141 293 HUMIL10_T8 (SEQ ID NO: 213) 285437

Segment cluster HUMIL10_N10 (SEQ ID NO:225) according to the presentinvention is supported by 1 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214). Table 223 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 223 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 1265

Segment cluster HUMIL10_N14 (SEQ ID NO:227) according to the presentinvention is supported by 57 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 224 below describes the starting and ending position of thissegment on each transcript.

TABLE 224 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 332789 HUMIL10_T5 (SEQ ID NO: 211) 489 946 HUMIL10_T6 (SEQ ID NO: 212) 360817 HUMIL10_T8 (SEQ ID NO: 213) 438 895

Segment cluster HUMIL10_N16 (SEQ ID NO:229) according to the presentinvention is supported by 20 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 225 below describes the starting and ending position of thissegment on each transcript.

TABLE 225 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 8151027 HUMIL10_T5 (SEQ ID NO: 211) 972 1184 HUMIL10_T6 (SEQ ID NO: 212)843 1055 HUMIL10_T8 (SEQ ID NO: 213) 921 1133

Segment cluster HUMIL10_N19 (SEQ ID NO:232) according to the presentinvention is supported by 18 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 226 below describes the starting and ending position of thissegment on each transcript.

TABLE 226 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 10461259 HUMIL10_T5 (SEQ ID NO: 211) 1203 1416 HUMIL10_T6 (SEQ ID NO: 212)1074 1287 HUMIL10_T8 (SEQ ID NO: 213) 1152 1365

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster HUMIL10_N1 (SEQ ID NO:221) according to the presentinvention is supported by 37 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T8 (SEQ ID NO:213). Table 227 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 227 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T8 (SEQ ID NO: 213) 210224

Segment cluster HUMIL10_N3 (SEQ ID NO:222) according to the presentinvention is supported by 38 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T5 (SEQ ID NO:211) and HUMIL10_T8 (SEQID NO:213). Table 228 below describes the starting and ending positionof this segment on each transcript.

TABLE 228 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T5 (SEQ ID NO: 211) 210269 HUMIL10_T8 (SEQ ID NO: 213) 225 284

Segment cluster HUMIL10_N11 (SEQ ID NO:226) according to the presentinvention is supported by 50 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211) and HUMIL10_T6 (SEQ ID NO:212). Table 229 below describes thestarting and ending position of this segment on each transcript.

TABLE 229 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 266331 HUMIL10_T5 (SEQ ID NO: 211) 423 488 HUMIL10_T6 (SEQ ID NO: 212) 294359

Segment cluster HUMIL10_N15 (SEQ ID NO:228) according to the presentinvention is supported by 18 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T100 (SEQ ID NO:214), HUMIL10_T5 (SEQID NO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 230 below describes the starting and ending position of thissegment on each transcript.

TABLE 230 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 790814 HUMIL10_T5 (SEQ ID NO: 211) 947 971 HUMIL10_T6 (SEQ ID NO: 212) 818842 HUMIL10_T8 (SEQ ID NO: 213) 896 920

Segment cluster HUMIL10_N17 (SEQ ID NO:230) according to the presentinvention is supported by 17 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 231 below describes the starting and ending position of thissegment on each transcript.

TABLE 231 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 10281031 HUMIL10_T5 (SEQ ID NO: 211) 1185 1188 HUMIL10_T6 (SEQ ID NO: 212)1056 1059 HUMIL10_T8 (SEQ ID NO: 213) 1134 1137

Segment cluster HUMIL10_N18 (SEQ ID NO:231) according to the presentinvention is supported by 17 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 232 below describes the starting and ending position of thissegment on each transcript.

TABLE 232 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 10321045 HUMIL10_T5 (SEQ ID NO: 211) 1189 1202 HUMIL10_T6 (SEQ ID NO: 212)1060 1073 HUMIL10_T8 (SEQ ID NO: 213) 1138 1151

Segment cluster HUMIL10_N20 (SEQ ID NO:233) according to the presentinvention is supported by 16 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 233 below describes the starting and ending position of thissegment on each transcript.

TABLE 233 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 12601341 HUMIL10_T5 (SEQ ID NO: 211) 1417 1498 HUMIL10_T6 (SEQ ID NO: 212)1288 1369 HUMIL10_T8 (SEQ ID NO: 213) 1366 1447

Segment cluster HUMIL10_N21 (SEQ ID NO:234) according to the presentinvention is supported by 14 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): HUMIL10_T10 (SEQ ID NO:214), HUMIL10_T5 (SEQ IDNO:211), HUMIL10_T6 (SEQ ID NO:212) and HUMIL10_T8 (SEQ ID NO:213).Table 234 below describes the starting and ending position of thissegment on each transcript.

TABLE 234 Segment location on transcripts Segment Segment Transcriptname starting position ending position HUMIL10_T10 (SEQ ID NO: 214) 13421458 HUMIL10_T5 (SEQ ID NO: 211) 1499 1615 HUMIL10_T6 (SEQ ID NO: 212)1370 1486 HUMIL10_T8 (SEQ ID NO: 213) 1448 1564

FIG. 34 shows the structure of the HUMIL10 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

Expression of Homo sapiens Interleukin 10 (IL10) HUMIL10 Transcriptswhich are Detectable by Amplicon as Depicted in Sequence NameHUMIL10_seg5 (SEQ ID NO:424) in Different Normal Tissues

Expression of Homo sapiens interleukin 10 (IL10) transcripts detectableby or according to seg5-HUMIL10 seg5 (SEQ ID NO:424) amplicon andprimers HUMIL10_seg5F (SEQ ID NO:425) and HUMIL10_seg5R (SEQ ID NO:426)was measured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the heart samples (samplenumbers 44, 45 and 46, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the heart samples asshown in FIG. 35A, or by the median of the blood samples (sample numbers51-53), to obtain a value of relative expression of each sample relativeto median of the blood samples as shown in FIG. 35B.

Forward Primer (HUMIL10_seg5F (SEQ ID NO:425)): TCTGGTGAAGGAGGATCGCTReverse Primer (HUMIL10_seg5R (SEQ ID NO:426)): GAGTGAGAGATTGGCGGAGGTAmplicon (HUMIL10_seg5 (SEQ ID NO:424)):TCTGGTGAAGGAGGATCGCTAGAACCAAGCTGTCCTCTTAAGCTAGTTGCAGCAGCCCCTCCTCCCAGCCACCTCCGCCAATCTCTCACTC

Expression of Homo sapiens interleukin 10 (IL10) HUMIL10 transcriptswhich are detectable by amplicon as depicted in sequence nameHUMIL10_seg0WT (SEQ ID NO:427) in different normal tissues

Expression of Homo sapiens interleukin 10 (IL10) transcripts detectableby or according to seg0WT—HUMIL10_seg0WT (SEQ ID NO:427) amplicon andprimers HUMIL10_seg0WTF (SEQ ID NO:428) and HUMIL10_seg0WTR (SEQ IDNO:429) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the heart samples (samplenumbers 44, 45 and 46, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the heart samples asshown in FIG. 36A, or by the median of the blood samples (sample numbers51-53), to obtain a value of relative expression of each sample relativeto median of the blood samples as shown in FIG. 36B.

Forward Primer (HUMIL10_seg0WTF (SEQ ID NO:428)): AAGAAGGCATGCACAGCTCAGReverse Primer (HUMIL10_seg0WTR (SEQ ID NO:429)): TCTCGAAGCATGTTAGGCAGGAmplicon (HUMIL10_seg0WT (SEQ ID NO:427)):AAGAAGGCATGCACAGCTCAGCACTGCTCTGTTGCCTGGTCCTCCTGACTGGGGTGAGGGCCAGCCCAGGCCAGGGCACCCAGTCTGAGAACAGCTGCACCCACTTCCCAGGCAACCTGCCTAACATGCTTCGAGA

Description for Cluster AA336074

Cluster AA336074 features 1 transcript(s) and 7 segment(s) of interest,the names for which are given in Tables 235 and 236, respectively. Theselected protein variants are given in table 237.

TABLE 235 Transcripts of interest Transcript Name AA336074_T20 (SEQ IDNO: 235)

TABLE 236 Segments of interest Segment Name AA336074_N4 (SEQ ID NO: 239)AA336074_N9 (SEQ ID NO: 240) AA336074_N28 (SEQ ID NO: 241) AA336074_N31(SEQ ID NO: 242) AA336074_N32 (SEQ ID NO: 243) AA336074_N0 (SEQ ID NO:237) AA336074_N2 (SEQ ID NO: 238)

TABLE 237 Proteins of interest Protein Name Corresponding Transcript(s)AA336074_P30 (SEQ ID NO: 236) AA336074_T20 (SEQ ID NO: 235)

These sequences are variants of the known protein Kallikrein 4 precursor(SwissProt accession identifier KLK4_HUMAN (SEQ ID NO:430) (SEQ ID NO:1029); known also according to the synonyms EC 3.4.21.-; Prostase;Kallikrein-like protein 1; KLK-L1; Enamel matrix serine proteinase 1),referred to herein as the previously known protein. Known polymorphismsfor this sequence are as shown in Table 238

TABLE 238 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 197 Q -> H

Protein Kallikrein 4 precursor localization is believed to be Secreted.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: proteolysis and peptidolysis,which are annotation(s) related to Biological Process; serine-typepeptidase activity, which are annotation(s) related to MolecularFunction; and extracellular region, which are annotation(s) related toCellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

According to optional embodiments of the present invention, variants ofthis cluster according to the present invention (amino acid and/ornucleic acid sequences of AA336074) may optionally have one or more ofthe following utilities, as described in greater detail below. It shouldbe noted that these utilities are optionally and preferably suitable forhuman and non-human animals as subjects, except where otherwise noted.The reasoning is described with regard to biological and/orphysiological and/or other information about the known protein, but isgiven to demonstrate particular diagnostic utility for the variantsaccording to the present invention.

A non-limiting example of such a utility is the detection, diagnosisand/or determination of diagnosis of prostate cancer. The methodcomprises detecting a AA336074 variant, for example a variant protein,protein fragment, peptide, polynucleotide, polynucleotide fragmentand/or oligonucleotide as described herein, optionally and preferably ina serum sample. The expression levels of the AA336074 variant asdetermined in a patient can be further compared to those in a normalindividual.

Involvement of the known Kallikrein 4 for the above utility is describedwith regard to EP Patent No. EP1294941B1, hereby incorporated byreference as if fully set forth herein.

Another non-limiting example of such a utility is detecting ormonitoring prostate or ovarian cancer in combination with humankallikrein 11. The method comprises detecting a AA336074 variant, forexample a variant protein, protein fragment, peptide, polynucleotide,polynucleotide fragment and/or oligonucleotide as described herein,optionally and preferably in a serum sample. The expression levels ofthe AA336074 variant as determined in a patient can be further comparedto those in a normal individual.

Differential expression of the known Kallikrein 4 for the aboveutilities is described with regard to US Patent Application No.US20040203012, hereby incorporated by reference as if fully set forthherein.

Another non-limiting example of such a utility is detecting ovariancancer in combination with KLK9. The method comprises detecting aAA336074 variant, for example a variant protein, protein fragment,peptide, polynucleotide, polynucleotide fragment and/or oligonucleotideas described herein, optionally and preferably in a serum sample. Theexpression levels of the AA336074 variant as determined in a patient canbe further compared to those in a normal individual.

Differential expression of the known Kallikrein 4 for the aboveutilities is described with regard to US Patent Application No.US20050176002, hereby incorporated by reference as if fully set forthherein.

Another non-limiting example of such a utility is diagnosing andmonitoring renal cell carcinoma. The method comprises detecting aAA336074 variant, for example a variant protein, protein fragment,peptide, polynucleotide, polynucleotide fragment and/or oligonucleotideas described herein, optionally and preferably in a serum sample. Theexpression levels of the AA336074 variant as determined in a patient canbe further compared to those in a normal individual.

Differential expression of the known Kallikrein 4 for the above utilityis described with regard to PCT Application No. WO 04/077060, herebyincorporated by reference as if fully set forth herein.

Another non-limiting example of such a utility is detecting endocrinecancer in combination with kallikrein 13. The method comprises detectinga AA336074 variant, for example a variant protein, protein fragment,peptide, polynucleotide, polynucleotide fragment and/or oligonucleotideas described herein, optionally and preferably in a serum sample. Theexpression levels of the AA336074 variant as determined in a patient canbe further compared to those in a normal individual.

Differential expression of the known Kallikrein 4 for the above utilityis described with regard to PCT Application No. WO 04/021009, herebyincorporated by reference as if fully set forth herein.

Another non-limiting example of such a utility is detecting breast orovarian cancer in combination with kallikrein 5. The method comprisesdetecting a AA336074 variant, for example a variant protein, proteinfragment, peptide, polynucleotide, polynucleotide fragment and/oroligonucleotide as described herein, optionally and preferably in aserum sample. The expression levels of the AA336074 variant asdetermined in a patient can be further compared to those in a normalindividual.

Differential expression of the known Kallikrein 4 for the above utilityis described with regard to PCT Application No. WO 04/021008, herebyincorporated by reference as if fully set forth herein.

Another non-limiting example of such a utility is detecting ovariancancer in combination with kallikrein 8. The method comprises detectinga AA336074 variant, for example a variant protein, protein fragment,peptide, polynucleotide, polynucleotide fragment and/or oligonucleotideas described herein, optionally and preferably in a serum sample. Theexpression levels of the AA336074 variant as determined in a patient canbe further compared to those in a normal individual.

Differential expression of the known Kallikrein 4 for the above utilityis described with regard to PCT Application No. WO 03/085404, herebyincorporated by reference as if fully set forth herein.

According to optional embodiments of the present invention, variants ofthis cluster according to the present invention (amino acid and/ornucleic acid sequences of AA336074) may optionally have one or more ofthe following utilities, as described with regard to the Table below. Itshould be noted that these utilities are optionally and preferablysuitable for human and non-human animals as subjects, except whereotherwise noted. The reasoning is described with regard to biologicaland/or physiological and/or other information about the known protein,but is given to demonstrate particular diagnostic utility for thevariants according to the present invention.

TABLE 239 Table of Utilities for Variants of AA336074, related toKallikrein 4: Utility Reason Reference Over expression in prostateOvesen J., et al., Acta Otolaryngol cancer (detection in serum Suppl.1992; 492: 113-4 and ICH). highly expressed for Veveris-Lowe TL., etal., Endocr diagnosis of serous ovarian Relat Cancer. 2005 12(3):631-43. carcinomas Higher expression indicates Dong Yet al., Clin CancerRes. 2001 poor prognosis of ovarian Aug; 7(8): 2363-71; Obiezu CV., etcancer patients al., Clin Cancer Res. 2001 Aug; 7(8): 2380-6theranostics marker for overexpression is an exclusion Xi Z., et al.,2004 94(1): 80-5. paclitaxel resistance in criteria for the treatment.ovarian cancer alteration in sequence and Stephanopoulos G., et al.,expression as markers for J Dent Res. 2005 84(12): 1117-26; amelogenesisimperfecta Ozdemir D. et al., J Dent Res. 2005 84(11): 1031-5; NaganoT., et al., J Dent Res. 200382(12): 982-6.

Other non-limiting exemplary utilities for AA336074 variants accordingto the present invention are described in greater detail below and alsowith regard to the previous section on clinical utility.

Cluster AA336074 can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of FIG. 37 refer to weightedexpression of ESTs in each category, as “parts per million” (ratio ofthe expression of ESTs for a particular cluster to the expression of allESTs in that category, according to parts per million).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 34 and Table 240. As shown in FIG. 37 clusterAA336074 is overexpressed (at least at a minimum level) in the followingpathological conditions: prostate cancer, a mixture of malignant tumorsfrom different tissues and epithelial malignant tumors.

TABLE 240 Normal tissue distribution Name of Tissue Number brain 0prostate 167 general 5 uterus 0 epithelial 13

TABLE 241 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 brain N/A 3.1e−01 N/A N/A 3.7e−01 2.7prostate 4.4e−01 5.7e−01 7.0e−08 3.4 6.5e−05 2.4 general 5.9e−04 5.0e−036.2e−29 11.0  6.1e−16 5.7 uterus 4.4e−01 3.7e−01 6.6e−01 1.5 6.4e−01 1.5epithelial 1.0e−02 5.8e−02 2.5e−15 6.2 3.7e−07 3.2

As noted above, cluster AA336074 features 1 transcript(s), which werelisted in Table 235 above. These transcript(s) encode for protein(s)which are variant(s) of protein Kallikrein 4 precursor. A description ofeach variant protein according to the present invention is now provided.

Variant protein AA336074_P30 (SEQ ID NO:236) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) AA336074_T20 (SEQ IDNO:235). An alignment is given to the known protein (Kallikrein 4precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between AA336074_P30 (SEQ ID NO:236) and KLK4_HUMAN(SEQ ID NO:430) (SEQ ID NO: 1029):

A. An isolated chimeric polypeptide as set forth in AA336074_P30 (SEQ IDNO:236), comprising a first amino acid sequence being at least 90%homologous toMATAGNPWGWFLGYLILGVAGSLVSGSCSQIINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVREPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLAN corresponding to amino acids 1-158 of KLK4_HUMAN (SEQ IDNO:430) (SEQ ID NO: 1029), which also corresponds to amino acids 1-158of AA336074_P30 (SEQ ID NO:236), and a second amino acid sequence beingat least 70%, optionally at least 80%, preferably at least 85%, morepreferably at least 90% and most preferably at least 95% homologous to apolypeptide having the sequenceDAVIAIQSQTVGGWECEKLSQPWQGCTISATSSARTSCCILTGCSLLLTASPGVEIRRDSAGCSHMIKEGPELGVTPDPS (SEQ ID NO: 493) corresponding to amino acids 159-238 ofAA336074_P30 (SEQ ID NO:236), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of AA336074_P30(SEQ ID NO:236), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceDAVIAIQSQTVGGWECEKLSQPWQGCTISATSSARTSCCILTGCSLLLTASPGVEIRRDSAGCSHMIKEGPELGVTPDPS (SEQ ID NO: 493) of AA336074_P30 (SEQ ID NO:236).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein AA336074_P30 (SEQ ID NO:236) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table242, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein AA336074_P30 (SEQ ID NO:236) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 242 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 22 S -> A 43 P -> T

The glycosylation sites of variant protein AA336074_P30 (SEQ ID NO:236),as compared to the known protein Kallikrein 4 precursor, are describedin Table 243 (given according to their position(s) on the amino acidsequence in the first column; the second column indicates whether theglycosylation site is present in the variant protein; and the lastcolumn indicates whether the position is different on the variantprotein).

TABLE 243 Glycosylation site(s) Position(s) on known amino acid Presentin Position(s) on sequence variant protein? variant protein 169 No

Variant protein AA336074_P30 (SEQ ID NO:236) is encoded by the followingtranscript(s): AA336074_T20 (SEQ ID NO:235), for which the codingportion starts at position 61 and ends at position 774. The transcriptalso has the following SNPs as listed in Table 244 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein AA336074_P30(SEQ ID NO:236) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 244 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence T -> G 124, 126 C -> A 187, 1651 C -> T  360 G -> A  525 C -> G1716 T -> C 1797

As noted above, cluster AA336074 features 7 segment(s), which werelisted in Table 236 above and for which the sequence(s) are given at theend of the application. These segment(s) are portions of nucleic acidsequence(s) which are described herein separately because they are ofparticular interest. A description of each segment according to thepresent invention is now provided.

Segment cluster AA336074_N4 (SEQ ID NO:239) according to the presentinvention is supported by 54 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 245 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 245 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 122284

Segment cluster AA336074_N9 (SEQ ID NO:240) according to the presentinvention is supported by 77 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 246 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 246 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 285535

Segment cluster AA336074_N28 (SEQ ID NO:241) according to the presentinvention is supported by 5 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 247 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 247 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 536691

Segment cluster AA336074_N31 (SEQ ID NO:242) according to the presentinvention is supported by 3 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 248 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 248 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 6921258

Segment cluster AA336074_N32 (SEQ ID NO:243) according to the presentinvention is supported by 8 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 249 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 249 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235)1259 1849

According to an optional embodiment of the present invention, shortsegments related to the above cluster are also provided. These segmentsare up to about 120 bp in length, and so are included in a separatedescription.

Segment cluster AA336074_N0 (SEQ ID NO:237) according to the presentinvention is supported by 1 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 250 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 250 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 149

Segment cluster AA336074_N2 (SEQ ID NO:238) according to the presentinvention is supported by 11 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): AA336074_T20 (SEQ ID NO:235). Table 251 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 251 Segment location on transcripts Segment Segment Transcriptname starting position ending position AA336074_T20 (SEQ ID NO: 235) 50121

FIG. 38 shows the structure of the AA336074 mRNA and protein variants.Exons are represented by white boxes, while introns are represented bytwo headed arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

Expression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_junc9-28 (SEQ ID NO:431) in Normaland Cancerous Breast Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according tojunc9-28—AA336074_junc9-28 (SEQ ID NO:431) amplicon and primersAA336074_junc9-28F (SEQ ID NO:432) and AA336074_junc9-28R (SEQ IDNO:433) was measured by real time PCR. In parallel the expression offour housekeeping genes—G6PD (GenBank Accession No. NM_(—)000402 (SEQ IDNO:405); G6PD (SEQ ID NO:404) amplicon), HPRT1 (GenBank Accession No.NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon (SEQ ID NO:380)),PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)) and SDHA (GenBank Accession No.NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ ID NO:365))was measured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the normal post-mortem orpost surgery (PM/PS) samples (sample numbers 57, 59, 60, 63, 66, 64, 56,65 and 67, Table 4 above), to obtain a value of fold up-regulation foreach sample relative to median of the normal PM samples.

FIG. 39 is a histogram showing over expression of the above-indicatedHomo sapiens kallikrein 4 (prostase, enamel matrix, prostate) (KLK4)transcripts in cancerous Breast samples relative to the normal samples.Values represent the average of duplicate experiments. Error barsindicate the minimal and maximal values obtained.

As is evident from FIG. 39, the expression of Homo sapiens kallikrein 4(prostase, enamel matrix, prostate) (KLK4) transcripts detectable by theabove amplicon in cancer samples was significantly higher than in thenon-cancerous samples (sample numbers 57, 59, 60, 63, 66, 64, 56, 65 and67, Table 4 above). Notably an over-expression of at least 5 fold wasfound in 12 out of 26 adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) transcriptsdetectable by the above amplicon in Breast cancer samples versus thenormal tissue samples was determined by T test as 1.88e-03.

Threshold of 5 fold over expression was found to differentiate betweencancer and normal samples with P value of 1.16e-02 as checked by exactFisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: AA336074_junc9-28F (SEQ ID NO:432) forward primer;and AA336074_junc9-28R (SEQ ID NO:433) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: AA336074_junc9-28 (SEQID NO:431).

Forward Primer (AA336074_junc9-28F (SEQ ID NO: 432)): CTGCTGGCGAACGATGCTReverse Primer (AA336074_junc9-28R (SEQ ID NO: 433)):GCCGAAATGGTACAACCCTG Amplicon (AA336074_junc9-28 (SEQ ID NO:431)):CTGCTGGCGAACGATGCTGTGATTGCCATCCAGTCCCAGACTGTGGGAGGCTGGGAGTGTGAGAAGCTTTCCCAACCCTGGCAGGGTTGTACCATTTCGG CExpression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_junc9-28 (SEQ ID NO:431) inDifferent Normal Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according tojunc9-28—AA336074_junc9-28 (SEQ ID NO:431) amplicon and primersAA336074_junc9-28F (SEQ ID NO:432) and AA336074_junc9-28R (SEQ IDNO:433) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the breast samples (samplenumbers 34 and 35, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the breast samples.

FIG. 40 is a histogram showing the expression of Homo sapiens kallikrein4 (prostase, enamel matrix, prostate) (KLK4) AA336074 transcripts whichare detectable by amplicon as depicted in sequence nameAA336074_junc9-28 (SEQ ID NO:431) in different normal tissues.

Forward Primer (AA336074_junc9-28F (SEQ ID NO: 432)): CTGCTGGCGAACGATGCTReverse Primer (AA336074_junc9-28R (SEQ ID NO: 433)):GCCGAAATGGTACAACCCTG Amplicon (AA336074_junc9-28 (SEQ ID NO:431)):CTGCTGGCGAACGATGCTGTGATTGCCATCCAGTCCCAGACTGTGGGAGGCTGGGAGTGTGAGAAGCTTTCCCAACCCTGGCAGGGTTGTACCATTTCGG CExpression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_seg13WT (SEQ ID NO:434) in Normaland Cancerous Breast Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according toseg13WT—AA336074_seg13WT (SEQ ID NO:434) amplicon and primersAA336074_seg13WTF (SEQ ID NO:435) and AA336074_seg13WTR (SEQ ID NO:436)was measured by real time PCR. In parallel the expression of fourhousekeeping genes—G6PD (GenBank Accession No. NM_(—)000402 (SEQ IDNO:405); G6PD (SEQ ID NO:404) amplicon), RPL19 (GenBank Accession No.NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon), PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)) was measured similarly.For each RT sample, the expression of the above amplicon was normalizedto the normalization factor calculated from the expression of thesehouse keeping genes as described in normalization method 2 in the“materials and methods” section. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalsamples (sample numbers 43, 45, 46, 47, 48, 49, 50, 51, 52, 54, 56, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68 and 69, Table 4_(—)1 above), toobtain a value of fold up-regulation for each sample relative to medianof the normal samples.

FIG. 41 is a histogram showing over expression of the above-indicatedHomo sapiens kallikrein 4 (prostase, enamel matrix, prostate) (KLK4)transcripts in cancerous Breast samples relative to the normal samples.

As is evident from FIG. 41, the expression of Homo sapiens kallikrein 4(prostase, enamel matrix, prostate) (KLK4) transcripts detectable by theabove amplicon in cancer samples was higher than in the non-canceroussamples (sample numbers 39-43, 45, 46, 47, 48, 49, 50, 51, 52, 54, 56,58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68 and 69, Table 4_(—)1 above).Notably an over-expression of at least 10 fold was found in 11 out of 53adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) transcriptsdetectable by the above amplicon in Breast cancer samples versus thenormal tissue samples was determined by T test as 9.12e-03.

Threshold of 10 fold over expression was found to differentiate betweencancer and normal samples with P value of 3.86e-02 as checked by exactFisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: AA336074_seg13WTF (SEQ ID NO:435) forward primer;and AA336074_seg13WTR (SEQ ID NO:436) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: AA336074_seg13WT (SEQID NO:434).

Forward Primer (AA336074_seg13WTF (SEQ ID NO: 435)): AATGCCTACCGTGCTGCAGReverse Primer (AA336074_seg13WTR (SEQ ID NO: 436)): CGGCGCAGAACATGCTGAmplicon (AA336074_seg13WT (SEQ ID NO:434)):AATGCCTACCGTGCTGCAGTGCGTGAACGTGTCGGTGGTGTCTGAGGAGGTCTGCAGTAAGCTCTATGACCCGCTGTACCACCCCAGCATGTTCTGCGCC G Forward Primer(AA336074_seg13WTF (SEQ ID NO:435): AATGCCTACCGTGCTGCAG Reverse Primer(AA336074_seg13WTR (SEQ ID NO:436): CGGCGCAGAACATGCTG Amplicon(AA336074_seg13WT (SEQ ID NO:434:AATGCCTACCGTGCTGCAGTGCGTGAACGTGTCGGTGGTGTCTGAGGAGGTCTGCAGTAAGCTCTATGACCCGCTGTACCACCCCAGCATGTTCTGCGCC GExpression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_seg13WT (SEQ ID NO:434) inDifferent Normal Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according toseg13WT—AA336074_seg13WT (SEQ ID NO:434) amplicon and primersAA336074_seg13WTF (SEQ ID NO:435) and AA336074_seg13WTR (SEQ ID NO:436)was measured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), and TATA box (GenBank Accession No. NM_(—)003194 (SEQ IDNO:371); TATA (SEQ ID NO:370) amplicon) was measured similarly. For eachRT sample, the expression of the above amplicon was normalized to thenormalization factor calculated from the expression of these housekeeping genes as described in normalization method 2 in the “materialsand methods” section. The normalized quantity of each RT sample was thendivided by the median of the quantities of the breast samples (samplenumbers 41, 42 and 43, Table 5_(—)1 above), to obtain a value ofrelative expression of each sample relative to median of the breastsamples.

Forward Primer (AA336074_seg13WTF (SEQ ID NO: 435)): AATGCCTACCGTGCTGCAGReverse Primer (AA336074_seg13WTR (SEQ ID NO: 436)): CGGCGCAGAACATGCTGAmplicon (AA336074_seg13WT (SEQ ID NO:434)):AATGCCTACCGTGCTGCAGTGCGTGAACGTGTCGGTGGTGTCTGAGGAGGTCTGCAGTAAGCTCTATGACCCGCTGTACCACCCCAGCATGTTCTGCGCC G

FIG. 42 is a histogram showing over expression of the Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) AA336074transcripts which are detectable by amplicon as depicted in sequencename AA336074_seg13WT (SEQ ID NO:434) in different normal tissues.

Expression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_junc9-28 (SEQ ID NO:431) in Normaland Cancerous Lung Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according tojunc9-28—AA336074_junc9-28 (SEQ ID NO:431) amplicon and primersAA336074_junc9-28F (SEQ ID NO:432) and AA336074_junc9-28R (SEQ IDNO:433) was measured by real time PCR. In parallel the expression offour housekeeping genes—G6PD (GenBank Accession No. NM_(—)000402 (SEQ IDNO:405); G6PD (SEQ ID NO:404) amplicon), HPRT1 (GenBank Accession No.NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon (SEQ ID NO:380)),PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)), SDHA (GenBank Accession No.NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ ID NO:365))and Ubiquitin (GenBank Accession No. BC000449 (SEQ ID NO:366);amplicon—Ubiquitin-amplicon (SEQ ID NO:367)) was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3 above), toobtain a value of fold up-regulation for each sample relative to medianof the normal PM samples.

FIG. 43 is a histogram showing over expression of the above-indicatedHomo sapiens kallikrein 4 (prostase, enamel matrix, prostate) (KLK4)transcripts in cancerous lung samples relative to the normal samples.

As is evident from FIG. 43, the expression of Homo sapiens kallikrein 4(prostase, enamel matrix, prostate) (KLK4) transcripts detectable by theabove amplicon in cancer samples was higher in several cancer samplesthan in the non-cancerous samples (sample numbers 47, 48, 49, 50, 90,91, 92, 93, 96, 97, 98 and 99, Table 3 above). Notably anover-expression of at least 5 fold was found in 10 out of 35 non-smallcell lung carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

Threshold of 5 fold over expression was found to differentiate betweencancer and normal samples with P value of 4.01e-02 as checked by exactFisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: AA336074_junc9-28F (SEQ ID NO:432) forward primer;and AA336074_junc9-28R (SEQ ID NO:433) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: AA336074_junc9-28 (SEQID NO:431).

Forward Primer (AA336074_junc9-28F (SEQ ID NO: 432)): CTGCTGGCGAACGATGCTReverse Primer (AA336074_junc9-28R (SEQ ID NO: 433)):GCCGAAATGGTACAACCCTG Amplicon (AA336074_junc9-28 (SEQ ID NO:431)):CTGCTGGCGAACGATGCTGTGATTGCCATCCAGTCCCAGACTGTGGGAGGCTGGGAGTGTGAGAAGCTTTCCCAACCCTGGCAGGGTTGTACCATTTCGG CExpression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_seg31 (SEQ ID NO:437) in Normaland Cancerous Breast Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according toseg31—AA336074_seg31 (SEQ ID NO:437) amplicon and primersAA336074_seg31F (SEQ ID NO:438) and AA336074_seg31R (SEQ ID NO:439) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes—G6PD (GenBank Accession No. NM_(—)000402 (SEQ IDNO:405); G6PD (SEQ ID NO:404) amplicon), RPL19 (GenBank Accession No.NM_(—)000981 (SEQ ID NO:369); RPL19 (SEQ ID NO:368) amplicon), PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)) was measured similarly.For each RT sample, the expression of the above amplicon was normalizedto the normalization factor calculated from the expression of thesehouse keeping genes as described in normalization method 2 in the“materials and methods” section. The normalized quantity of each RTsample was then divided by the median of the quantities of the normalsamples (sample numbers 43, 45, 46, 47, 48, 49, 50, 51, 52, 54, 56, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68 and 69, Table 4_(—)1 above), toobtain a value of fold up-regulation for each sample relative to medianof the normal samples.

FIG. 44 is a histogram showing over expression of the above-indicatedHomo sapiens kallikrein 4 (prostase, enamel matrix, prostate) (KLK4)transcripts in cancerous Breast samples relative to the normal samples.

As is evident from FIG. 44, the expression of Homo sapiens kallikrein 4(prostase, enamel matrix, prostate) (KLK4) transcripts detectable by theabove amplicon in cancer samples was significantly higher than in thenon-cancerous samples (sample numbers 39-43, 45, 46, 47, 48, 49, 50, 51,52, 54, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68 and 69, Table4_(—)1 above). Notably an over-expression of at least 15 fold was foundin 25 out of 53 adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) transcriptsdetectable by the above amplicon in Breast cancer samples versus thenormal tissue samples was determined by T test as 5.54e-05.

Threshold of 15 fold over expression was found to differentiate betweencancer and normal samples with P value of 2.49e-06 as checked by exactFisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: AA336074_seg31F (SEQ ID NO:438) forward primer;and AA336074_seg31R (SEQ ID NO:439) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: AA336074_seg31 (SEQ IDNO:437).

Forward Primer (AA336074_seg31F (SEQ ID NO:438)): CTGGGTGCAGCCACATGATAReverse Primer (AA336074_seg31R (SEQ ID NO:439)): CCAGGTGGAAGTCGCTAGGAAmplicon (AA336074_seg31 (SEQ ID NO:437)):CTGGGTGCAGCCACATGATAAAGGAAGGACCGGAGCTTGGTGTAACCCCTGATCCCTCCTAGATGGGGCTAGGTGGGGCTAGCCTAGATGGGGCTAAGTC CTAGCGACTTCCACCTGGExpression of Homo sapiens Kallikrein 4 (Prostase, Enamel Matrix,Prostate) (KLK4) AA336074 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name AA336074_seg31 (SEQ ID NO:437) in DifferentNormal Tissues

Expression of Homo sapiens kallikrein 4 (prostase, enamel matrix,prostate) (KLK4) transcripts detectable by or according toseg31—AA336074_seg31 (SEQ ID NO:437) amplicon and primersAA336074_seg31F (SEQ ID NO:438) and AA336074_seg31R (SEQ ID NO:439) wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), and TATA box (GenBank Accession No. NM_(—)003194 (SEQ IDNO:371); TATA (SEQ ID NO:370) amplicon) was measured similarly. For eachRT sample, the expression of the above amplicon was normalized to thenormalization factor calculated from the expression of these housekeeping genes as described in normalization method 2 in the “materialsand methods” section. The normalized quantity of each RT sample was thendivided by the median of the quantities of the breast samples (samplenumbers 41, 42 and 43, Table 5_(—)1 above), to obtain a value ofrelative expression of each sample relative to median of the breastsamples.

Forward Primer (AA336074_seg31F (SEQ ID NO:438)): CTGGGTGCAGCCACATGATAReverse Primer (AA336074_seg31R (SEQ ID NO:439)): CCAGGTGGAAGTCGCTAGGAAmplicon (AA336074_seg31 (SEQ ID NO:437)):CTGGGTGCAGCCACATGATAAAGGAAGGACCGGAGCTTGGTGTAACCCCTGATCCCTCCTAGATGGGGCTAGGTGGGGCTAGCCTAGATGGGGCTAAGTC CTAGCGACTTCCACCTGG

FIG. 45 is a histogram showing over expression of the Homo sapienskallikrein 4 (prostase, enamel matrix, prostate) (KLK4) AA336074transcripts which are detectable by amplicon as depicted in sequencename AA336074_seg31 (SEQ ID NO:437) in different normal tissues.

Homo sapiens kallikrein 4 ((KLK4) AA336074 transcripts which aredetectable by amplicon as depicted in sequence name AA336074_junc9-28(SEQ ID NO:431) and primers AA336074_junc9-28F (SEQ ID NO:432) andAA336074_junc9-28R (SEQ ID NO:433) did not show any differentialexpression in one experiment carried out with each of the followingcancer panels: colon cancer and ovary cancer.

Homo sapiens kallikrein 4 ((KLK4) AA336074 transcripts which aredetectable by amplicon as depicted in sequence name AA336074_seg31 (SEQID NO:437) and primers AA336074_seg31F (SEQ ID NO:438) andAA336074_seg31R (SEQ ID NO:439) did not show any differential expressionin one experiment carried out with each of the following cancer panels:colon cancer, lung cancer and ovary cancer.

Description for Cluster HUMTREFAC

Cluster HUMTREFAC features 1 transcript(s) and 6 segment(s) of interest,the names for which are given in Tables 252 and 253, respectively. Theselected protein variants are given in table 254.

TABLE 252 Transcripts of interest Transcript Name HUMTREFAC_T3 (SEQ IDNO: 244)

TABLE 253 Segments of interest Segment Name HUMTREFAC_N0 (SEQ ID NO:246) HUMTREFAC_N9 (SEQ ID NO: 251) HUMTREFAC_N3 (SEQ ID NO: 247)HUMTREFAC_N4 (SEQ ID NO: 248) HUMTREFAC_N5 (SEQ ID NO: 249) HUMTREFAC_N8(SEQ ID NO: 250)

TABLE 254 Proteins of interest Protein Name Corresponding Transcript(s)HUMTREFAC_P9 (SEQ ID NO: 245) HUMTREFAC_T3 (SEQ ID NO: 244)

These sequences are variants of the known protein Trefoil factor 3precursor (SwissProt accession identifier TFF3_HUMAN (SEQ ID NO:440);known also according to the synonyms Intestinal trefoil factor; hP1.B),referred to herein as the previously known protein.

Protein Trefoil factor 3 precursor is known or believed to have thefollowing function(s): May have a role in promoting cell migration(motogen). Known polymorphisms for this sequence are as shown in Table255.

TABLE 255 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 74-76 QEA -> TRKT

Protein Trefoil factor 3 precursor localization is believed to beSecreted.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: defense response; digestion,which are annotation(s) related to Biological Process; and extracellularregion, which are annotation(s) related to Cellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

Cluster HUMTREFAC can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of FIG. 46 refer to weightedexpression of ESTs in each category, as “parts per million” (ratio ofthe expression of ESTs for a particular cluster to the expression of allESTs in that category, according to parts per million).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 39 and Table 256. FIG. 46 shows that clusterHUMTREFAC is overexpressed (at least at a minimum level) in thefollowing pathological conditions: a mixture of malignant tumors fromdifferent tissues, pancreas carcinoma, prostate cancer, breast malignanttumors and epithelial malignant tumors.

TABLE 256 Normal tissue distribution Name of Tissue Number lung 54general 38 Thyroid 255 muscle 3 pancreas 2 uterus 53 colon 772 liver 0prostate 15 lymph nodes 3 breast 0 stomach 0 adrenal 39 epithelial 94

TABLE 257 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 lung 4.3e−01 7.2e−01 3.9e−03 1.1 2.0e−01 0.5general 8.3e−05 2.0e−02 4.7e−28 3.5 3.0e−10 1.9 Thyroid 6.9e−01 6.9e−019.7e−01 0.5 9.7e−01 0.5 muscle 9.2e−01 4.8e−01 N/A N/A 4.0e−01 2.1pancreas 9.7e−02 2.1e−01 5.7e−03 6.5 2.1e−02 4.6 uterus 3.6e−01 6.9e−017.3e−02 1.3 4.0e−01 0.8 colon 1.8e−01 2.5e−01 9.6e−01 0.5 1.0e+00 0.4liver N/A 6.9e−01 N/A N/A 7.0e−01 1.4 prostate 1.1e−01 2.1e−01 1.3e−097.8 3.7e−07 5.5 lymph nodes 5.8e−01 8.2e−01 2.3e−02 5.0 1.9e−01 2.1breast 7.6e−02 1.5e−01 2.7e−06 12.2 1.0e−03 6.5 stomach 2.7e−01 1.0e−015.0e−01 2.0 6.5e−02 2.8 adrenal 6.1e−01 6.6e−01 7.0e−01 1.1 7.8e−01 0.9epithelial 9.5e−03 2.2e−01 1.0e−09 2.0 4.9e−02 1.1

As noted above, cluster HUMTREFAC features 1 transcript(s), which werelisted in Table 252 above. These transcript(s) encode for protein(s)which are variant(s) of protein Trefoil factor 3 precursor. Adescription of each variant protein according to the present inventionis now provided.

Variant protein HUMTREFAC_P9 (SEQ ID NO:245) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) HUMTREFAC_T3 (SEQ IDNO:244).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein HUMTREFAC_P9 (SEQ ID NO:245) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table258, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein HUMTREFAC_P9 (SEQ ID NO:245) sequence provides supportfor the deduced sequence of this variant protein according to thepresent invention).

TABLE 258 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 5 A -> S 5 A -> T 14 A -> V 60 P -> S 102 P ->123 S -> *

Variant protein HUMTREFAC_P9 (SEQ ID NO:245) is encoded by the followingtranscript(s): HUMTREFAC_T3 (SEQ ID NO:244), for which the codingportion starts at position 278 and ends at position 688. The transcriptalso has the following SNPs as listed in Table 259 (given according totheir position on the nucleotide sequence, with the alternative nucleicacid listed; the presence of known SNPs in variant protein HUMTREFAC_P9(SEQ ID NO:245) sequence provides support for the deduced sequence ofthis variant protein according to the present invention).

TABLE 259 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence A -> G 233 G -> A 290 G -> T 290, 589 C -> T 318, 455, 404, 685C -> 583 C -> A 645

1. Comparison Report Between HUMTREFAC_P9 (SEQ ID NO:245) and TFF3_HUMAN(SEQ ID NO:440):

A. An isolated chimeric polypeptide as set forth in HUMTREFAC_P9 (SEQ IDNO:245), comprising a first amino acid sequence being at least 90%homologous to MAARALCMLGLVLALLSSSSAEEYVGLS corresponding to amino acids1-28 of TFF3_HUMAN (SEQ ID NO:440), which also corresponds to aminoacids 1-28 of HUMTREFAC_P9 (SEQ ID NO:245), and a second amino acidsequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECLGVSSPCRKQNAPSEAPPAAPGRGMRGSEHPCPAVIAARHCSSQLFCPFAPGKRFC (SEQ ID NO: 501) corresponding toamino acids 29-137 of HUMTREFAC_P9 (SEQ ID NO:245), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for an edge portion of HUMTREFAC_P9(SEQ ID NO:245), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECLGVSSPCRKQNAPSEAPPAAPGRGMRGSEHPCPAVIAARHCSSQLFCPFAPGKRFC (SEQ ID NO: 501) of HUMTREFACQP9(SEQ ID NO:245).

2. Comparison Report Between HUMTREFAC_P9 (SEQ ID NO:245) andQ96NX0_HUMAN (SEQ ID NO: 554):

A. An isolated chimeric polypeptide as set forth in HUMTREFAC_P9 (SEQ IDNO:245), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequenceMAARALCMLGLVLALLSSSSAEEYVGLSQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECL (SEQ ID NO: 591) corresponding to amino acids 29-137 ofHUMTREFAC_P9 (SEQ ID NO:245), and a second amino acid sequence being atleast 90% homologous to ANQCAVPAKDRVDCGYPHVTPKE corresponding to aminoacids 51-78 of Q96NX0_HUMAN (SEQ ID NO: 554), which also corresponds toamino acids 1-28 of HUMTREFAC_P9 (SEQ ID NO:245), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of HUMTREFAC_P9 (SEQ IDNO:245), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequenceMAARALCMLGLVLALLSSSSAEEYVGLSQQGLWQLTGLCLGQLQTSVPCQPRTGWTAATPMSPPRSATTGAAALTPGSLECL (SEQ ID NO: 591) of HUMTREFAC_P9 (SEQ ID NO:245).

C. An isolated chimeric polypeptide encoding for an edge portion ofHUMTREFAC_P9 (SEQ ID NO:245), comprising a polypeptide having a length“n”, wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise LG, having a structure as follows: asequence starting from any of amino acid numbers 137−x to 137; andending at any of amino acid numbers 1+((n−2)−x), in which x varies from0 to n−2.

FIG. 47 shows mRNA and protein structure of HUMTREFAC variants. Exonsare represented by white boxes, while introns are represented by twoheaded arrows. Proteins are shown in boxes with upper right to lowerleft fill. The unique regions are represented by white boxes with dashedframe.

Description for Cluster Z22012

Cluster Z22012 features 2 transcript(s) and 49 segment(s) of interest,the names for which are given in Tables 260 and 261, respectively. Theselected protein variants are given in table 262.

TABLE 260 Transcripts of interest Transcript Name Z22012_T24 (SEQ ID NO:252) Z22012_T32 (SEQ ID NO: 253)

TABLE 261 Segments of interest Segment Name Z22012_N0 (SEQ ID NO: 256)Z22012_N34 (SEQ ID NO: 274) Z22012_N40 (SEQ ID NO: 279) Z22012_N41 (SEQID NO: 280) Z22012_N62 (SEQ ID NO: 301) Z22012_N1 (SEQ ID NO: 257)Z22012_N2 (SEQ ID NO: 258) Z22012_N3 (SEQ ID NO: 259) Z22012_N9 (SEQ IDNO: 260) Z22012_N10 (SEQ ID NO: 261) Z22012_N15 (SEQ ID NO: 262)Z22012_N16 (SEQ ID NO: 263) Z22012_N17 (SEQ ID NO: 264) Z22012_N18 (SEQID NO: 265) Z22012_N19 (SEQ ID NO: 266) Z22012_N22 (SEQ ID NO: 267)Z22012_N23 (SEQ ID NO: 268) Z22012_N29 (SEQ ID NO: 269) Z22012_N30 (SEQID NO: 270) Z22012_N31 (SEQ ID NO: 271) Z22012_N32 (SEQ ID NO: 272)Z22012_N33 (SEQ ID NO: 273) Z22012_N35 (SEQ ID NO: 275) Z22012_N37 (SEQID NO: 276) Z22012_N38 (SEQ ID NO: 277) Z22012_N39 (SEQ ID NO: 278)Z22012_N42 (SEQ ID NO: 281) Z22012_N43 (SEQ ID NO: 282) Z22012_N44 (SEQID NO: 283) Z22012_N45 (SEQ ID NO: 284) Z22012_N46 (SEQ ID NO: 285)Z22012_N47 (SEQ ID NO: 286) Z22012_N48 (SEQ ID NO: 287) Z22012_N49 (SEQID NO: 288) Z22012_N50 (SEQ ID NO: 289) Z22012_N51 (SEQ ID NO: 290)Z22012_N52 (SEQ ID NO: 291) Z22012_N53 (SEQ ID NO: 292) Z22012_N54 (SEQID NO: 293) Z22012_N55 (SEQ ID NO: 294) Z22012_N56 (SEQ ID NO: 295)Z22012_N57 (SEQ ID NO: 296) Z22012_N58 (SEQ ID NO: 297) Z22012_N59 (SEQID NO: 298) Z22012_N60 (SEQ ID NO: 299) Z22012_N61 (SEQ ID NO: 300)Z22012_N63 (SEQ ID NO: 302) Z22012_N64 (SEQ ID NO: 303) Z22012_N65 (SEQID NO: 304)

TABLE 262 Proteins of interest Protein Name Corresponding Transcript(s)Z22012_P41 (SEQ ID NO: 254) Z22012_T24 (SEQ ID NO: 252) Z22012_P42 (SEQID NO: 255) Z22012_T32 (SEQ ID NO: 253)

These sequences are variants of the known protein Galectin-3 bindingprotein precursor (SwissProt accession identifier L3BP_HUMAN (SEQ ID NO:441); known also according to the synonyms Lectin galactoside-bindingsoluble 3 binding protein; Mac-2 binding protein; Mac-2 BP; MAC2BP;Tumor-associated antigen 90K), referred to herein as the previouslyknown protein.

Protein Galectin-3 binding protein precursor is known or believed tohave the following function(s): Promotes integrin-mediated celladhesion. May stimulate host defense against viruses and tumor cells.Protein Galectin-3 binding protein precursor localization is believed tobe Secreted and extracellular matrix.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: cellular defense response;signal transduction, which are annotation(s) related to BiologicalProcess; scavenger receptor activity, which are annotation(s) related toMolecular Function; and extracellular space, which are annotation(s)related to Cellular Component.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

Cluster Z22012 can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of FIG. 48 refer to weightedexpression of ESTs in each category, as “parts per million” (ratio ofthe expression of ESTs for a particular cluster to the expression of allESTs in that category, according to parts per million).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 48 and Table 263. FIG. 48 shows that cluster Z22012is overexpressed (at least at a minimum level) in the followingpathological conditions: brain malignant tumors, pancreas carcinoma,hepatocellular carcinoma, prostate cancer, a mixture of malignant tumorsfrom different tissues and myosarcoma.

TABLE 263 Normal tissue distribution Name of Tissue Number brain 94ovary 662 bladder 164 lung 229 pancreas 12 liver 48 prostate 49 T cells0 adrenal 277 general 191 bone marrow 94 Thyroid 178 skin 257 muscle 41uterus 267 colon 533 kidney 181 lymph nodes 54 breast 285 head and neck131 stomach 469 epithelial 254 bone 379

TABLE 264 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 brain 1.6e−01 1.4e−01 6.6e−09 3.2 3.4e−18 2.7ovary 6.4e−01 5.6e−01 2.2e−02 0.6 1.4e−01 0.6 bladder 2.0e−01 3.6e−018.1e−03 2.7 9.8e−02 1.7 lung 9.5e−02 1.3e−01 1.5e−02 1.4 4.5e−03 1.6pancreas 1.7e−02 1.2e−02 1.7e−12 14.7 1.5e−16 16.4 liver 9.1e−01 4.9e−011.0e+00 0.5 7.3e−04 4.4 prostate 1.5e−01 2.0e−01 1.4e−03 3.6 4.5e−04 3.1T cells 5.0e−01 3.3e−01 3.3e−01 3.1 5.2e−01 1.8 adrenal 5.9e−01 5.1e−017.1e−01 0.7 7.8e−01 0.7 general 4.6e−05 4.0e−04 1.8e−31 2.0 2.8e−54 2.2bone marrow 7.6e−01 8.6e−01 1.6e−08 2.9 2.2e−02 0.7 Thyroid 6.0e−016.0e−01 4.9e−01 1.1 4.9e−01 1.1 skin 5.0e−01 6.6e−01 8.3e−01 0.6 1.5e−061.5 muscle 4.0e−01 2.6e−01 9.4e−09 4.2 2.6e−08 7.1 uterus 3.0e−012.7e−01 4.9e−02 0.9 3.5e−01 0.8 colon 1.3e−01 1.6e−01 9.4e−01 0.62.6e−03 0.5 kidney 6.2e−01 6.6e−01 7.5e−02 1.4 3.4e−02 1.4 lymph nodes7.4e−01 8.4e−01 2.3e−02 1.5 2.7e−01 0.8 breast 7.0e−01 7.2e−01 3.8e−010.7 1.3e−01 1.1 head and neck 3.4e−01 2.5e−01 1.0e+00 0.7 3.4e−02 1.6stomach 2.4e−01 2.0e−01 8.0e−01 0.3 6.4e−01 0.8 epithelial 1.3e−023.3e−02 4.3e−09 1.5 2.9e−18 1.8 bone 2.4e−01 1.5e−01 9.9e−01 0.4 7.6e−010.7

As noted above, cluster Z22012 features 2 transcript(s), which werelisted in Table 260 above. These transcript(s) encode for protein(s)which are variant(s) of protein Galectin-3 binding protein precursor. Adescription of each variant protein according to the present inventionis now provided.

Variant protein Z22012_P41 (SEQ ID NO:254) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z22012_T24 (SEQ ID NO:252).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z22012_P41 (SEQ ID NO:254) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table265, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z22012_P41 (SEQ ID NO:254) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 265 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 9 V -> M 17 Q -> 17 Q -> L 34 Q -> 68 E -> *128 P -> 135 G ->

The glycosylation sites of variant protein Z22012_P41 (SEQ ID NO:254),as compared to the known protein Galectin-3 binding protein precursor,are described in Table 266 (given according to their position(s) on theamino acid sequence in the first column; the second column indicateswhether the glycosylation site is present in the variant protein; andthe last column indicates whether the position is different on thevariant protein).

TABLE 266 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 69 Yes 69125 Yes 125 192 No 362 No 398 No 551 No 580 No

Variant protein Z22012_P41 (SEQ ID NO:254) is encoded by the followingtranscript(s): Z22012_T24 (SEQ ID NO:252), for which the coding portionstarts at position 310 and ends at position 777. The transcript also hasthe following SNPs as listed in Table 267 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z22012_P41 (SEQ IDNO:254) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 267 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence A -> 187, 359, 2230 G -> C 198, 2270, 2456 G -> T 198, 511,1519, 1582, 1819 G -> A 246, 334, 1602, 2037, 2190, 2257 G -> 246, 411,712, 1582, 1602, 2037, 2257 A -> T 351, 359, 1961 C -> T 369, 399, 576,1303, 1446, 1926, 2014, 2118, 2154, 2178, 2295, 2310, 2322, 2406, 2615 C-> 691, 1345, 1353, 1361, 1433, 1706, 1708 -> G 841, 1269, 1999 -> C 852 -> T  902 C -> A 1303, 2202, 2216, 2310, C -> G 1433, 1706, 1708,2225, 2393 T -> C 1610, 2477, 2635, T -> 1610 T -> A 1739, 2477, 2641 A-> G 1961, 2433 A -> C 2546 T -> G 2641

Variant protein Z22012_P42 (SEQ ID NO:255) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z22012_T32 (SEQ ID NO:253).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z22012_P42 (SEQ ID NO:255) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table268, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z22012_P42 (SEQ ID NO:255) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 268 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 9 V -> M 17 Q -> 17 Q -> L 34 Q -> 68 E -> *175 C -> 178 T -> 181 P -> 205 P -> 205 P -> A

The glycosylation sites of variant protein Z22012_P42 (SEQ ID NO:255),as compared to the known protein Galectin-3 binding protein precursor,are described in Table 269 (given according to their position(s) on theamino acid sequence in the first column; the second column indicateswhether the glycosylation site is present in the variant protein; andthe last column indicates whether the position is different on thevariant protein).

TABLE 269 Glycosylation site(s) Position(s) on known Present amino acidsequence in variant protein? Position(s) on variant protein 69 Yes 69125 Yes 125 192 No 362 No 398 No 551 No 580 No

Variant protein Z22012_P42 (SEQ ID NO:255) is encoded by the followingtranscript(s): Z22012_T32 (SEQ ID NO:253), for which the coding portionstarts at position 310 and ends at position 924. The transcript also hasthe following SNPs as listed in Table 270 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z22012_P42 (SEQ IDNO:255) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 270 Nucleic acid SNPs Polymorphism SNP position(s) on nucleotidesequence A -> 187, 359, 1719 G -> C 198, 1759, 1945 G -> T 198, 511,1008, 1071, 1308 G -> A 246, 334, 1091, 1526, 1679, 1746 G -> 246, 411,1071, 1091, 1488, 1526, 1746 A -> T 351, 359, 1450 C -> T 369, 399, 576,792, 935, 1503, 1607, 1643, 1667, 1784, 1415, 1799, 1811, 1895, 2104 ->G  758 C -> A 792, 1691, 1705, 1799 C -> 834, 842, 850, 922, 1195, 1197C -> G 922, 1195, 1197, 1714, 1882 T -> C 1099, 1966, 2124 T -> 1099 T-> A 1228, 1966, 2130 A -> G 1450, 1922 A -> C 2035 T -> G 2130

1. Comparison Report Between Z22012_P41 (SEQ ID NO:254) and L3BP_HUMAN(SEQ ID NO: 441):

A. An isolated chimeric polypeptide as set forth in Z22012_P41 (SEQ IDNO:254), comprising a first amino acid sequence being at least 90%homologous toMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRBERDAGVVCTN corresponding toamino acids 1-125 of L3BP_HUMAN (SEQ ID NO: 441), which also correspondsto amino acids 1-125 of Z22012_P41 (SEQ ID NO:254), and a second aminoacid sequence being at least 70%, optionally at least 80%, preferably atleast 85%, more preferably at least 90% and most preferably at least 95%homologous to a polypeptide having the sequenceGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 499) corresponding to aminoacids 126-156 of Z22012_P41 (SEQ ID NO:254), wherein said first aminoacid sequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of Z22012_P41(SEQ ID NO:254), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO:499) of Z22012_P41 (SEQ ID NO:254).

2. Comparison Report Between Z22012_P41 (SEQ ID NO:254) and NP_(—)005558(SEQ ID NO: 551):

A. An isolated chimeric polypeptide as set forth in Z22012_P41 (SEQ IDNO:254), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASWCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRBERDAGVVCTNGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 589) corresponding to amino acids 126-156 ofZ22012_P41 (SEQ ID NO:254), and a second amino acid sequence being atleast 90% homologous toFQTPQHPSFLFQDKRVSWSLVYLPTIQSCWNYGFSCSSDELPVLGLTKSGGSDRTIAYENKALMLCEGLFVADVTDFEGWKAAIPSALDTNSSKSTSSFPCPAGHFNGFRTVIRPFYLTNSSGVD corresponding toamino acids 1-125 of NP_(—)005558 (SEQ ID NO: 551), which alsocorresponds to amino acids 1-125 of Z22012_P41 (SEQ ID NO:254), whereinsaid first amino acid sequence and second amino acid sequence arecontiguous and in a sequential order.

B. An isolated polypeptide encoding for a head of Z22012_P41 (SEQ IDNO:254), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGAPTPWTSPGSSRRPLARSLTASGAATCPSA (SEQ ID NO: 589) of Z22012_P41 (SEQ ID NO:254).

1. Comparison Report Between Z22012_P42 (SEQ ID NO:255) and L3BP_HUMAN(SEQ ID NO: 441):

A. An isolated chimeric polypeptide as set forth in Z22012_P42 (SEQ IDNO:255), comprising a first amino acid sequence being at least 70%,optionally at least 80%, preferably at least 85%, more preferably atleast 90% and most preferably at least 95%, homologous to a polypeptidehaving the sequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ IDNO: 590) corresponding to amino acids 126-205 of Z22012_P42 (SEQ IDNO:255), and a second amino acid sequence being at least 90% homologoustoFQTPQHPSFLFQDKRVSWSLVYLPTIQSCWNYGFSCSSDELPVLGLTKSGGSDRTIAYENKALMLCEGLFVADVTDFEGWKAAIPSALDTNSSKSTSSFPCPAGHFNGFRTVIRPFYLTNSSGVD corresponding toamino acids 1-125 of L3BP_HUMAN (SEQ ID NO: 441), which also correspondsto amino acids 1-125 of Z22012_P42 (SEQ ID NO:255), wherein said firstamino acid sequence and second amino acid sequence are contiguous and ina sequential order.

B. An isolated polypeptide encoding for a head of Z22012_P42 (SEQ IDNO:255), comprising a polypeptide being at least 70%, optionally atleast about 80%, preferably at least about 85%, more preferably at leastabout 90% and most preferably at least about 95% homologous to thesequenceMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTNGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ IDNO: 590) of Z22012_P42 (SEQ ID NO:255).

2. Comparison Report Between Z22012_P42 (SEQ ID NO:255) and NP_(—)005558(SEQ ID NO: 551):

A. An isolated chimeric polypeptide as set forth in Z22012_P42 (SEQ IDNO:255), comprising a first amino acid sequence being at least 90%homologous toMTPPRLFWVWLLVAGTQGVNDGDMRLADGGATNQGRVEIFYRGQWGTVCDNLWDLTDASVVCRALGFENATQALGRAAFGQGSGPIMLDEVQCTGTEASLADCKSLGWLKSNCRHERDAGVVCTN corresponding toamino acids 1-125 of NP_(—)005558 (SEQ ID NO: 551), which alsocorresponds to amino acids 1-125 of Z22012_P42 (SEQ ID NO:255), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ ID NO: 500) corresponding to amino acids 126-205 ofZ22012_P42 (SEQ ID NO:255), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of Z22012_P42(SEQ ID NO:255), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceGTSTPEGLTSPCRQSSASTSWPLPMGPGSCRATAQASLPSSSPRTPRSRCPWTCMPMQWPQGTPCWRSSAYSSWPGTSRP (SEQ ID NO: 500) of Z22012_P42 (SEQ ID NO:255).

Description for Cluster Z39737

Cluster Z39737 features 2 transcript(s) and 31 segment(s) of interest,the names for which are given in Tables 271 and 272, respectively. Theselected protein variants are given in table 273.

TABLE 271 Transcripts of interest Transcript Name Z39737_T5 (SEQ ID NO:305) Z39737_T20 (SEQ ID NO: 306)

TABLE 272 Segments of interest Segment Name Z39737_N14 (SEQ ID NO: 320)Z39737_N20 (SEQ ID NO: 325) Z39737_N24 (SEQ ID NO: 327) Z39737_N27 (SEQID NO: 328) Z39737_N38 (SEQ ID NO: 339) Z39737_N2 (SEQ ID NO: 309)Z39737_N3 (SEQ ID NO: 310) Z39737_N4 (SEQ ID NO: 311) Z39737_N5 (SEQ IDNO: 312) Z39737_N6 (SEQ ID NO: 313) Z39737_N7 (SEQ ID NO: 314) Z39737_N9(SEQ ID NO: 315) Z39737_N10 (SEQ ID NO: 316) Z39737_N11 (SEQ ID NO: 317)Z39737_N12 (SEQ ID NO: 318) Z39737_N13 (SEQ ID NO: 319) Z39737_N15 (SEQID NO: 321) Z39737_N16 (SEQ ID NO: 322) Z39737_N17 (SEQ ID NO: 323)Z39737_N18 (SEQ ID NO: 324) Z39737_N21 (SEQ ID NO: 326) Z39737_N28 (SEQID NO: 329) Z39737_N29 (SEQ ID NO: 330) Z39737_N30 (SEQ ID NO: 331)Z39737_N31 (SEQ ID NO: 332) Z39737_N32 (SEQ ID NO: 333) Z39737_N33 (SEQID NO: 334) Z39737_N34 (SEQ ID NO: 335) Z39737_N35 (SEQ ID NO: 336)Z39737_N36 (SEQ ID NO: 337) Z39737_N37 (SEQ ID NO: 338)

TABLE 273 Proteins of interest Protein Name Corresponding Transcript(s)Z39737_P9 (SEQ ID NO: 307) Z39737_T20 (SEQ ID NO: 306) Z39737_P25 (SEQID NO: 308) Z39737_T5 (SEQ ID NO: 305)

These sequences are variants of the known protein Spondin 2 precursor(SwissProt accession identifier SPO2_HUMAN (SEQ ID NO: 442; known alsoaccording to the synonyms Mindin; Differentially expressed in cancerousand noncancerous lung cells 1; DIL-1; UNQ435/PRO866), referred to hereinas the previously known protein.

Protein Spondin 2 precursor is known or believed to have the followingfunction(s): Cell adhesion protein that promote adhesion and outgrowthof hippocampal embryonic neurons. Binds directly to bacteria and theircomponents and functions as an opsonin for macrophage phagocytosis ofbacteria. Essential in the initiation of the innate immune response andrepresents a unique pattern-recognition molecule in the ECM formicrobial pathogens (By similarity). Known polymorphisms for thissequence are as shown in Table 274.

TABLE 274 Amino acid mutations for Known Protein SNP position(s) onamino acid sequence Comment 40 P -> L (in dbSNP: 922697). /FTId =VAR_019701 122 E -> A (in dbSNP: 11247975). /FTId = VAR_019702 242 L ->V (in dbSNP: 2279279). /FTId = VAR_019703

Protein Spondin 2 precursor localization is believed to be Secreted;extracellular matrix (By similarity).

Cluster Z39737 can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of FIG. 49 refer to weightedexpression of ESTs in each category, as “parts per million” (ratio ofthe expression of ESTs for a particular cluster to the expression of allESTs in that category, according to parts per million).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 49 and Table 275. FIG. 49 shows that cluster Z39737is overexpressed (at least at a minimum level) in the followingpathological conditions: prostate cancer.

TABLE 275 Normal tissue distribution Name of Tissue Number brain 13ovary 116 bladder 82 lung 61 pancreas 10 prostate 97 general 51 skin 152uterus 233 colon 39 kidney 35 breast 0 head and neck 0 stomach 39epithelial 74 bone 94

TABLE 276 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 brain 1.9e−01 3.8e−01 3.7e−01 1.7 7.2e−01 0.9ovary 8.8e−01 8.9e−01 9.9e−01 0.3 1.0e+00 0.3 bladder 7.0e−01 7.8e−014.7e−01 1.1 7.1e−01 0.8 lung 8.8e−01 8.8e−01 1.0e+00 0.1 9.9e−01 0.4pancreas 1.9e−01 3.4e−01 1.2e−02 3.9 4.8e−02 2.8 prostate 1.2e−011.7e−01 2.9e−10 4.8 1.7e−07 3.6 general 3.3e−02 4.1e−01 2.8e−12 2.03.8e−03 1.2 skin 7.3e−01 8.0e−01 8.5e−01 0.7 1.0e+00 0.2 uterus 7.0e−018.3e−01 1.0e+00 0.3 1.0e+00 0.2 colon 6.6e−01 7.5e−01 7.8e−01 0.88.6e−01 0.7 kidney 3.8e−01 6.3e−01 1.3e−02 2.7 8.0e−02 1.8 breast1.1e−01 2.2e−01 3.2e−01 2.5 5.6e−01 1.7 head and neck 2.1e−01 1.7e−01N/A N/A 1.4e−01 1.6 stomach 5.8e−01 8.4e−01 3.1e−01 1.4 7.3e−01 0.8epithelial 3.3e−01 8.3e−01 3.0e−07 1.8 7.7e−02 1.0 bone 6.6e−01 6.7e−018.7e−01 0.6 9.3e−01 0.6

As noted above, cluster Z39737 features 2 transcript(s), which werelisted in Table 271 above. These transcript(s) encode for protein(s)which are variant(s) of protein Spondin 2 precursor. A description ofeach variant protein according to the present invention is now provided.

Variant protein Z39737_P9 (SEQ ID NO:307) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z39737_T20 (SEQ ID NO:306).An alignment is given to the known protein (Spondin 2 precursor) in thealignment table on the attached CD-ROM. A brief description of therelationship of the variant protein according to the present inventionto each such aligned protein is as follows:

1. Comparison Report Between Z39737_P9 (SEQ ID NO:307) andSPO2_HUMAN_V1:

A. An isolated chimeric polypeptide as set forth in Z39737_P9 (SEQ IDNO:307), comprising a first amino acid sequence being at least 90%homologous toMENPSPAAALGKALCALLLATLGAAGQPLGGESICSARAPAKYSITFTGKWSQTAFPKQYPLFRPPAQWSSLLGAAHSSDYSMWRKNQYVSNGLRDFAERGEAWALMKEIEAAGEALQSVHAVFSAPAVPSGTGQTcorresponding to amino acids 1-136 of SPO2_HUMAN_V1, which alsocorresponds to amino acids 1-136 of Z39737_P9 (SEQ ID NO:307), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceFLQQGCPPSPGVPTGFPGASYSATMWEF RDLSGSSGSYVETRNSSP (SEQ ID NO: 494)corresponding to amino acids 137-185 of Z39737_P9 (SEQ ID NO:307),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of Z39737_P9(SEQ ID NO:307), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceFLQQGCPPSPGVPTGFPGASYSATMWEFHHHRDLSGSSGSYVETRNSSP (SEQ ID NO: 494) ofZ39737_P9 (SEQ ID NO:307).

It should be noted that the known protein sequence (SPO2_HUMAN (SEQ IDNO: 442) has one or more changes than the sequence given at the end ofthe application and named as being the amino acid sequence forSPO2_HUMAN_V1. These changes were previously known to occur and arelisted in the table below.

TABLE 277 Changes to SPO2_HUMAN_V1 SNP position on amino acid sequenceType of change 122 variant

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z39737_P9 (SEQ ID NO:307) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table278, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z39737_P9 (SEQ ID NO:307) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 278 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 25 A -> 38 R -> G 40 P -> L 99 E -> 122 A -> E136 T -> 156 S -> P

Variant protein Z39737_P9 (SEQ ID NO:307) is encoded by the followingtranscript(s): Z39737_T20 (SEQ ID NO:306), for which the coding portionstarts at position 321 and ends at position 875. The transcript also hasthe following SNPs as listed in Table 279 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z39737_P9 (SEQ IDNO:307) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 279 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence A -> 28, 111, 726, 1339 G -> 51, 617, 1379, 1426, 1602 C ->394, 1275 G -> A 416, 1035, 1325 A -> G 432, 1222 C -> T 439, 1110,1175, 1370, 1647 C -> A 685, 1792 T -> C 786, 1124, 1138 G -> C 1379 A-> C 1791

Variant protein Z39737_P25 (SEQ ID NO:308) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z39737_T5 (SEQ ID NO:305).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z39737_P25 (SEQ ID NO:308) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table280, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z39737_P25 (SEQ ID NO:308) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 280 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 25 A -> 38 R -> G 40 P -> L

Variant protein Z39737_P25 (SEQ ID NO:308) is encoded by the followingtranscript(s): Z39737_T5 (SEQ ID NO:305), for which the coding portionstarts at position 321 and ends at position 641. The transcript also hasthe following SNPs as listed in Table 281 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z39737_P25 (SEQ IDNO:308) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 281 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence A -> 28, 111 G -> 51, 982, 1476, 1805, 1852, 2028 C -> 394,1449, 1701 G -> A 416, 1378, 1751 A -> G 432, 1648 C -> T 439, 664,1536, 1601, 1796, 2073 G -> C 593, 1409, 1805 C -> A 1050, 2218 A ->1091, 1765 T -> A 1137 -> T 1231 C -> G 1235, 1449 T -> C 1550, 1564 A-> C 2217

FIG. 50 shows mRNA and Protein Structure of Z39737 variants. Exons arerepresented by white boxes, while introns are represented by two headedarrows. Proteins are shown in boxes with upper right to lower left fill.The unique regions are represented by white boxes with dashed frame.

Description for Cluster Z25299

Cluster Z25299 features 5 transcript(s) and 9 segment(s) of interest,the names for which are given in Tables 282 and 283, respectively. Theselected protein variants are given in table 284.

TABLE 282 Transcripts of interest Transcript Name Z25299_T1 (SEQ ID NO:340) Z25299_T2 (SEQ ID NO: 341) Z25299_T5 (SEQ ID NO: 342) Z25299_T6(SEQ ID NO: 343) Z25299_T9 (SEQ ID NO: 344)

TABLE 283 Segments of interest Segment Name Z25299_N8 (SEQ ID NO: 350)Z25299_N13 (SEQ ID NO: 352) Z25299_N16 (SEQ ID NO: 354) Z25299_N17 (SEQID NO: 355) Z25299_N18 (SEQ ID NO: 356) Z25299_N20 (SEQ ID NO: 357)Z25299_N21 (SEQ ID NO: 358) Z25299_N12 (SEQ ID NO: 351) Z25299_N15 (SEQID NO: 353)

TABLE 284 Proteins of interest Protein Name Corresponding Transcript(s)Z25299_P1 (SEQ ID NO: 345) Z25299_T1 (SEQ ID NO: 340) Z25299_P4 (SEQ IDNO: 346) Z25299_T5 (SEQ ID NO: 342) Z25299_P5 (SEQ ID NO: 347) Z25299_T6(SEQ ID NO: 343) Z25299_P6 (SEQ ID NO: 348) Z25299_T2 (SEQ ID NO: 341)Z25299_P8 (SEQ ID NO: 349) Z25299_T9 (SEQ ID NO: 344)

These sequences are variants of the known protein Antileukoproteinase 1precursor (SwissProt accession identifier ALK1_HUMAN (SEQ ID NO:443);known also according to the synonyms ALP; HUSI-1; Seminal proteinaseinhibitor; Secretory leukocyte protease inhibitor; BLPI; Mucusproteinase inhibitor; MPI; WAP four-disulfide core domain protein 4;Protease inhibitor WAP4), referred to herein as the previously knownprotein.

Protein Antileukoproteinase 1 precursor is known or believed to have thefollowing function(s): Acid-stable proteinase inhibitor with strongaffinities for trypsin, chymotrypsin, elastase, and cathepsin G. Mayprevent elastase-mediated damage to oral and possibly other mucosaltissues. Protein Antileukoproteinase 1 precursor localization isbelieved to be Secreted.

The previously known protein also has the following indication(s) and/orpotential therapeutic use(s): Unspecified. It has been investigated forclinical/therapeutic use in humans, for example as a target for anantibody or small molecule, and/or as a direct therapeutic; availableinformation related to these investigations is as follows. Potentialpharmaceutically related or therapeutically related activity oractivities of the previously known protein are as follows: Elastaseinhibitor; Tryptase inhibitor. A therapeutic role for a proteinrepresented by the cluster has been predicted. The cluster was assignedthis field because there was information in the drug database or thepublic databases (e.g., described herein above) that this protein, orpart thereof, is used or can be used for a potential therapeuticindication: Anti-inflammatory; Antiasthma; Recombinant, other.

The following GO Annotation(s) apply to the previously known protein.The following annotation(s) were found: endopeptidase inhibitoractivity, which are annotation(s) related to Molecular Function.

The GO assignment relies on information from one or more of theSwissProt/TremBl Protein knowledgebase, available from<http://www.expasy.ch/sprot/>; or Locuslink, available from<http://www.ncbi.nlm.nih.gov/projects/LocusLink/>.

Cluster Z25299 can be used as a diagnostic marker according tooverexpression of transcripts of this cluster in cancer. Expression ofsuch transcripts in normal tissues is also given according to thepreviously described methods. The term “number” in the left hand columnof the table and the numbers on the y-axis of the FIG. 51 refer toweighted expression of ESTs in each category, as “parts per million”(ratio of the expression of ESTs for a particular cluster to theexpression of all ESTs in that category, according to parts permillion).

Overall, the following results were obtained as shown with regard to thehistograms in FIG. 51 and Table 285. This cluster is overexpressed (atleast at a minimum level) in the following pathological conditions:brain malignant tumors, ovarian carcinoma and a mixture of malignanttumors from different tissues.

TABLE 285 Normal tissue distribution Name of Tissue Number brain 4 ovary0 bladder 82 lung 440 pancreas 20 liver 68 prostate 35 general 71 skin214 uterus 112 colon 39 kidney 28 breast 51 stomach 180 head and neck636 epithelial 140 bone 6

TABLE 286 P values and ratios for expression in cancerous tissue Name ofTissue P1 P2 SP1 R3 SP2 R4 brain 2.2e−01 3.8e−01 8.0e−03 3.6 6.6e−02 1.8ovary 3.7e−02 3.0e−02 1.0e−02 5.6 6.5e−03 5.2 bladder 8.2e−01 8.5e−019.2e−01 0.6 9.7e−01 0.5 lung 6.9e−01 8.5e−01 9.6e−01 0.5 1.0e+00 0.3pancreas 3.4e−01 3.2e−01 3.6e−01 1.7 3.9e−01 1.5 liver 4.1e−01 9.2e−014.2e−02 3.2 6.5e−01 0.8 prostate 9.1e−01 9.2e−01 8.9e−01 0.5 9.4e−01 0.5general 2.5e−03 1.8e−01 1.4e−06 1.6 4.8e−01 0.9 skin 5.1e−01 7.6e−019.3e−01 0.4 1.0e+00 0.1 uterus 1.3e−01 9.8e−02 4.0e−02 1.6 3.3e−01 1.1colon 3.8e−01 3.2e−01 4.1e−01 1.5 4.2e−01 1.4 kidney 7.4e−01 8.4e−012.0e−01 2.0 4.1e−01 1.4 breast 5.0e−01 6.1e−01 9.6e−02 1.6 3.4e−01 1.1stomach 1.4e−01 6.4e−01 8.6e−01 0.7 9.9e−01 0.4 head and neck 3.0e−015.2e−01 8.0e−01 0.6 1.0e+00 0.3 epithelial 1.1e−01 6.1e−01 3.4e−01 1.01.0e+00 0.6 bone 5.5e−01 7.3e−01 4.0e−01 2.1 4.9e−01 1.6

As noted above, cluster Z25299 features 5 transcript(s), which werelisted in Table 282 above. These transcript(s) encode for protein(s)which are variant(s) of protein Antileukoproteinase 1 precursor. Adescription of each variant protein according to the present inventionis now provided.

Variant protein Z25299_P1 (SEQ ID NO:345) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z25299_T1 (SEQ ID NO:340).An alignment is given to the known protein (Antileukoproteinase 1precursor) at in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between Z25299_P1 (SEQ ID NO:345) and ALK1_HUMAN(SEQ ID NO:443):

A. An isolated chimeric polypeptide as set forth in Z25299_P1 (SEQ IDNO:345), comprising a first amino acid sequence being at least 90%homologous toMKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLMLNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPVK correspondingto amino acids 1-131 of ALK1 HUMAN (SEQ ID NO:443), which alsocorresponds to amino acids 1-131 of Z25299_P1 (SEQ ID NO:345), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGKQGMRAH (SEQ ID NO: 495) corresponding to amino acids 132-139 ofZ25299_P1 (SEQ ID NO:345), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of Z25299_P1(SEQ ID NO:345), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GKQGMRAH (SEQ ID NO: 495) of Z25299_P1 (SEQID NO:345).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z25299_P1 (SEQ ID NO:345) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table287, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z25299_P1 (SEQ ID NO:345) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 287 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 15 L -> 43 C -> R 48 K -> N 83 R -> K 136 M ->T

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 288:

TABLE 288 InterPro domain(s) Domain description Analysis typePosition(s) on protein Whey acidic protein, core region FPrintScan28-37, 50-57, 57-66, 121-129 Whey acidic protein, core region HMMPfam31-75, 85-129 Whey acidic protein, core region HMMSmart 31-76, 85-130Whey acidic protein, core region ScanRegExp 51-64, 105-118

Variant protein Z25299_P1 (SEQ ID NO:345) is encoded by the followingtranscript(s): Z25299_T1 (SEQ ID NO:340), for which the coding portionstarts at position 124 and ends at position 540. The transcript also hasthe following SNPs as listed in Table 289 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z25299_P1 (SEQ IDNO:345) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 289 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 147, 166, 339, 435, 989, 1127 C -> 166 T -> C 250, 530,851 A -> G 267 A -> C 267, 1162, 1180, 1183, 1216 G -> A 371, 1262

Variant protein Z25299_P4 (SEQ ID NO:346) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z25299_T5 (SEQ ID NO:342).An alignment is given to the known protein (Antileukoproteinase 1precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between Z25299_P4 (SEQ ID NO:346) and ALK1_HUMAN(SEQ ID NO:443):

A. An isolated chimeric polypeptide as set forth in Z25299_P4 (SEQ IDNO:346), comprising a first amino acid sequence being at least 90%homologous toMKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLMLNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPVK correspondingto amino acids 1-131 of ALK1_HUMAN (SEQ ID NO:443), which alsocorresponds to amino acids 1-131 of Z25299_P4 (SEQ ID NO:346), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGCFSPSISPSHFFTMSSISTFSAVLRTSASSLSACVLPATHQMRSGEEFSTFGFMLVLK (SEQ ID NO:496) corresponding to amino acids 132-190 of Z25299_P4 (SEQ ID NO:346),wherein said first amino acid sequence and second amino acid sequenceare contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of Z25299_P4(SEQ ID NO:346), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequenceGCFSPSISPSHFFTMSSISTFSAVLRTSASSLSACVLPATHQMRSGEEFSTFGFMLVLK (SEQ ID NO:496) of Z25299_P4 (SEQ ID NO:346).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z25299_P4 (SEQ ID NO:346) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table290, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z25299_P4 (SEQ ID NO:346) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 290 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 15 L -> 43 C -> R 48 K -> N 83 R -> K

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 291:

TABLE 291 InterPro domain(s) Domain description Analysis typePosition(s) on protein Whey acidic protein, core region FPrintScan28-37, 50-57, 57-66, 121-129 Whey acidic protein, core region HMMPfam31-75, 85-129 Whey acidic protein, core region HMMSmart 31-76, 85-130Whey acidic protein, core region ScanRegExp 51-64, 105-118

Variant protein Z25299_P4 (SEQ ID NO:346) is encoded by the followingtranscript(s): Z25299_T5 (SEQ ID NO:342), for which the coding portionstarts at position 124 and ends at position 693. The transcript also hasthe following SNPs as listed in Table 292 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z25299_P4 (SEQ IDNO:346) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 292 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 147, 166, 339, 435 C -> 166 T -> C 250 A -> G 267 A -> C267 G -> A 371

Variant protein Z25299_P5 (SEQ ID NO:347) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z25299_T6 (SEQ ID NO:343).An alignment is given to the known protein (Antileukoproteinase 1precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between Z25299_P5 (SEQ ID NO:347) and ALK1_HUMAN(SEQ ID NO:443):

A. An isolated chimeric polypeptide as set forth in Z25299_P5 (SEQ IDNO:347), comprising a first amino acid sequence being at least 90%homologous toMKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLMLNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPVK correspondingto amino acids 1-131 of ALK1_HUMAN (SEQ ID NO:443), which alsocorresponds to amino acids 1-131 of Z25299_P5 (SEQ ID NO:347), and asecond amino acid sequence being at least 70%, optionally at least 80%,preferably at least 85%, more preferably at least 90% and mostpreferably at least 95% homologous to a polypeptide having the sequenceGEKRHHKQLRDQEVDPLEMRRHSAG (SEQ ID NO: 497) corresponding to amino acids132-156 of Z25299_P5 (SEQ ID NO:347), wherein said first amino acidsequence and second amino acid sequence are contiguous and in asequential order.

B. An isolated polypeptide encoding for an edge portion of Z25299_P5(SEQ ID NO:347), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence GEKRHHKQLRDQEVDPLEMRRHSAG (SEQ ID NO: 497) ofZ25299_P5 (SEQ ID NO:347).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z25299_P5 (SEQ ID NO:347) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table293, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z25299_P5 (SEQ ID NO:347) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 293 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 15 L -> 43 C -> R 48 K -> N 83 R -> K

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 294:

TABLE 294 InterPro domain(s) Domain description Analysis typePosition(s) on protein Whey acidic protein, core region FPrintScan28-37, 50-57, 57-66, 121-129 Whey acidic protein, core region HMMPfam31-75, 85-129 Whey acidic protein, core region HMMSmart 31-76, 85-130Whey acidic protein, core region ScanRegExp 51-64, 105-118

Variant protein Z25299_P5 (SEQ ID NO:347) is encoded by the followingtranscript(s): Z25299_T6 (SEQ ID NO:343), for which the coding portionstarts at position 124 and ends at position 591. The transcript also hasthe following SNPs as listed in Table 295 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z25299_P5 (SEQ IDNO:347) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 295 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 147, 166, 339, 435, C -> 166 T -> C 250 A -> G 267 A ->C 267 G -> A 371

Variant protein Z25299_P6 (SEQ ID NO:348) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z25299_T2 (SEQ ID NO:341).An alignment is given to the known protein (Antileukoproteinase 1precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between Z25299_P6 (SEQ ID NO:348) and ALK1_HUMAN(SEQ ID NO:443):

A. An isolated chimeric polypeptide as set forth in Z25299_P6 (SEQ IDNO:348), comprising a first amino acid sequence being at least 90%homologous toMKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNP corresponding to amino acids 1-81 of ALK1_HUMAN (SEQ IDNO:443), which also corresponds to amino acids 1-81 of Z25299_P6 (SEQ IDNO:348), and a second amino acid sequence being at least 70%, optionallyat least 80%, preferably at least 85%, more preferably at least 90% andmost preferably at least 95% homologous to a polypeptide having thesequence RGSLGSAQ (SEQ ID NO: 498) corresponding to amino acids 82-89 ofZ25299_P6 (SEQ ID NO:348), wherein said first amino acid sequence andsecond amino acid sequence are contiguous and in a sequential order.

B. An isolated polypeptide encoding for an edge portion of Z25299_P6(SEQ ID NO:348), comprising an amino acid sequence being at least 70%,optionally at least about 80%, preferably at least about 85%, morepreferably at least about 90% and most preferably at least about 95%homologous to the sequence RGSLGSAQ (SEQ ID NO: 498) of Z25299_P6 (SEQID NO:348).

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z25299_P6 (SEQ ID NO:348) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table296, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z25299_P6 (SEQ ID NO:348) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 296 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 15 L -> 43 C -> R 48 K -> N

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 297:

TABLE 297 InterPro domain(s) Domain description Analysis typePosition(s) on protein Whey acidic protein, core region FPrintScan28-37, 50-57, 57-66, 67-75 Whey acidic protein, core region HMMPfam31-75 Whey acidic protein, core region HMMSmart 31-76 Whey acidicprotein, core region ScanRegExp 51-64

Variant protein Z25299_P6 (SEQ ID NO:348) is encoded by the followingtranscript(s): Z25299_T2 (SEQ ID NO:341), for which the coding portionstarts at position 124 and ends at position 390. The transcript also hasthe following SNPs as listed in Table 298 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z25299_P6 (SEQ IDNO:348) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 298 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 147, 166, 399, 431, 541 C -> 166 T -> C 250 A -> G 267 A-> C 267, 576, 594, 597, 630 G -> A 676

Variant protein Z25299_P8 (SEQ ID NO:349) according to the presentinvention has an amino acid sequence as given at the end of theapplication; it is encoded by transcript(s) Z25299_T9 (SEQ ID NO:344).An alignment is given to the known protein (Antileukoproteinase 1precursor) in the alignment table on the attached CD-ROM. A briefdescription of the relationship of the variant protein according to thepresent invention to each such aligned protein is as follows:

1. Comparison Report Between Z25299_P8 (SEQ ID NO:349) and ALK1_HUMAN(SEQ ID NO:443):

A. An isolated chimeric polypeptide as set forth in Z25299_P8 (SEQ IDNO:349), comprising a amino acid sequence being at least 90% homologoustoMKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPT corresponding to amino acids 1-82 of ALK1_HUMAN (SEQ IDNO:443), which also corresponds to amino acids 1-82 of Z25299_P8 (SEQ IDNO:349), wherein said and first amino acid sequence are contiguous andin a sequential order.

B. An isolated chimeric polypeptide encoding for an edge portion ofZ25299_P8 (SEQ ID NO:349), comprising a polypeptide having a length “n”,wherein n is at least about 10 amino acids in length, optionally atleast about 20 amino acids in length, preferably at least about 30 aminoacids in length, more preferably at least about 40 amino acids in lengthand most preferably at least about 50 amino acids in length, wherein atleast two amino acids comprise T, having a structure as follows: asequence starting from any of amino acid numbers 82−x to 82; and endingat any of amino acid numbers 82+((n−2)−x), in which x varies from 0 ton−2.

The localization of the variant protein was determined according toresults from a number of different software programs and analyses,including analyses from SignalP and other specialized programs. Thevariant protein is secreted.

Variant protein Z25299_P8 (SEQ ID NO:349) also has the followingnon-silent SNPs (Single Nucleotide Polymorphisms) as listed in Table299, (given according to their position(s) on the amino acid sequence,with the alternative amino acid(s) listed; the presence of known SNPs invariant protein Z25299_P8 (SEQ ID NO:349) sequence provides support forthe deduced sequence of this variant protein according to the presentinvention).

TABLE 299 Amino acid mutations SNP position(s) on amino acid sequenceAlternative amino acid(s) 15 L -> 43 C -> R 48 K -> N

The variant protein has the following domains, as determined by usingInterPro. The domains are described in Table 300:

TABLE 300 InterPro domain(s) Domain description Analysis typePosition(s) on protein Whey acidic protein, core region FPrintScan28-37, 50-57, 57-66, 67-75 Whey acidic protein, core region HMMPfam31-75 Whey acidic protein, core region HMMSmart 31-76 Whey acidicprotein, core region ScanRegExp 51-64

Variant protein Z25299_P8 (SEQ ID NO:349) is encoded by the followingtranscript(s): Z25299_T9 (SEQ ID NO:344), for which the coding portionstarts at position 124 and ends at position 369. The transcript also hasthe following SNPs as listed in Table 301 (given according to theirposition on the nucleotide sequence, with the alternative nucleic acidlisted; the presence of known SNPs in variant protein Z25299_P8 (SEQ IDNO:349) sequence provides support for the deduced sequence of thisvariant protein according to the present invention).

TABLE 301 Nucleic acid SNPs SNP position(s) on nucleotide Polymorphismsequence C -> T 147, 166, 339, 395 C -> 166 T -> C 250 A -> G 267 A -> C267, 430, 448, 451, 484 G -> A 530

As noted above, cluster Z25299 features 9 segment(s), which were listedin Table 283 above and for which the sequence(s) are given. Thesesegment(s) are portions of nucleic acid sequence(s) which are describedherein separately because they are of particular interest. A descriptionof segments 13, 17, 18 and 20 according to the present invention is nowprovided.

Segment cluster Z25299_N13 (SEQ ID NO:352) according to the presentinvention is supported by 266 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): Z25299_T1 (SEQ ID NO:340), Z25299_T2 (SEQ IDNO:341), Z25299_T5 (SEQ ID NO:342), Z25299_T6 (SEQ ID NO:343) andZ25299_T9 (SEQ ID NO:344). Table 302 below describes the starting andending position of this segment on each transcript.

TABLE 302 Segment location on transcripts Segment Segment Transcriptname starting position ending position Z25299_T1 (SEQ ID NO: 340) 246367 Z25299_T2 (SEQ ID NO: 341) 246 367 Z25299_T5 (SEQ ID NO: 342) 246367 Z25299_T6 (SEQ ID NO: 343) 246 367 Z25299_T9 (SEQ ID NO: 344) 246367

Segment cluster Z25299_N17 (SEQ ID NO:355) according to the presentinvention is supported by 6 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): Z25299_T1 (SEQ ID NO:340). Table 303 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 303 Segment location on transcripts Segment Segment Transcriptname starting position ending position Z25299_T1 (SEQ ID NO: 340) 5181099

Segment cluster Z25299_N18 (SEQ ID NO:356) according to the presentinvention is supported by 178 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): Z25299_T1 (SEQ ID NO:340), Z25299_T2 (SEQ IDNO:341) and Z25299_T9 (SEQ ID NO:344). Table 304 below describes thestarting and ending position of this segment on each transcript.

TABLE 304 Segment location on transcripts Segment Segment Transcriptname starting position ending position Z25299_T1 (SEQ ID NO: 340) 11001282 Z25299_T2 (SEQ ID NO: 341) 514 696 Z25299_T9 (SEQ ID NO: 344) 368550

Segment cluster Z25299_N20 (SEQ ID NO:357) according to the presentinvention is supported by 2 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): Z25299_T6 (SEQ ID NO:343). Table 305 belowdescribes the starting and ending position of this segment on eachtranscript.

TABLE 305 Segment location on transcripts Segment Segment Transcriptname starting position ending position Z25299_T6 (SEQ ID NO: 343) 518707

Microarray (chip) data is also available for this segment as follows. Asdescribed above with regard to the cluster itself, variousoligonucleotides were tested for being differentially expressed invarious disease conditions, particularly cancer. The followingoligonucleotides were found to hit this segment, shown in Table 306.

TABLE 306 Oligonucleotides related to this segment Overexpressed in ChipOligonucleotide name cancers reference Z25299_0_3_0 (SEQ ID NO: 458)ovarian carcinoma OVAThe sequence of the oligonucleotide Z25299_(—)0_(—)3_(—)0 (SEQ IDNO:458) is given.

>Z25299_0_3_0 (SEQ ID NO:458)AACTCTGGCACCTTGGGCTGTGGAAGGCTCTGGAAAGTCCTTCAAAGCTG

Segment cluster Z25299_N15 (SEQ ID NO:353) according to the presentinvention is supported by 233 libraries. The number of libraries wasdetermined as previously described. This segment can be found in thefollowing transcript(s): Z25299_T1 (SEQ ID NO:340), Z25299_T5 (SEQ IDNO:342) and Z25299_T6 (SEQ ID NO:343). Table 307 below describes thestarting and ending position of this segment on each transcript.

TABLE 307 Segment location on transcripts Segment Segment Transcriptname starting position ending position Z25299_T1 (SEQ ID NO: 340) 368371 Z25299_T5 (SEQ ID NO: 342) 368 371 Z25299_T6 (SEQ ID NO: 343) 368371

FIG. 52 shows mRNA and Protein Structure of Z25299 variants. Exons arerepresented by white boxes, while introns are represented by two headedarrows. Proteins are shown in boxes with upper right to lower left fill.The unique regions are represented by white boxes with dashed frame. Aconversion table for the nodes listed in table 283 used for amplicons asdescribed below is given in Table 308 below:

TABLE 308 Amplicons names Corresponding amplicon names based on (as usedbelow (POS)) Table 272 above (DDS) Seg 20 seg 17 Seg 23 seg 20 junc13-14-21 Junc 13-18Expression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_junc13-14-21 (SEQ IDNO:444) in Different Normal Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg23—Z25299_junc13-14-21 (SEQ ID NO:444) amplicon and primers Z25299junc13-14-21F (SEQ ID NO: 445) and Z25299_junc13-14-21R (SEQ ID NO: 446)was measured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the ovary samples (samplenumbers 19 and 20, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the ovary samples.

Forward Primer (Z25299_junc13-14-21F (SEQ ID NO: 445)):ACCCCAAACCCAACTTGATTC Reverse Primer (Z25299_junc13-14-21R (SEQ ID NO:446)): TCAGTGGTGGAGCCAAGTCTC Amplicon (Z25299_s junc13-14-21 (SEQ ID NO:444)): ACCCCAAACCCAACTTGATTCCTGCCATATGGAGGAGGCTCTGGAGTCCTGCTCTGTGTGGTCCAGGTCCTTTCCACCCTGAGACTTGGCTCCACCACTG A

FIG. 53 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_junc13-14-21 (SEQ ID NO:444) in different normal tissues.

Expression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg12-13WT (SEQ ID NO:447)in Different Normal Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg12-13WT—Z25299_seg12-13WT (SEQ ID NO:447) amplicon and primersZ25299_seg12-13WTF (SEQ ID NO:448) and Z25299_seg12-13WTR (SEQ IDNO:449) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM 004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBankAccession No. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQID NO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the ovary samples (samplenumbers 19 and 20, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the ovary samples.

Forward Primer (Z25299_seg12-13WTF (SEQ ID NO: 448)):AAGAAATCTGCCCAGTGCCT Reverse Primer (Z25299_seg12-13WTR (SEQ ID NO:449)): TTGATGCCACAAGTGTCAGGA Amplicon (Z25299_seg12-13WT (SEQ IDNO:447)): AAGAAATCTGCCCAGTGCCTTAGATACAAGAAACCTGAGTGCCAGAGTGACTGGCAGTGTCCAGGGAAGAAGAGATGTTGTCCTGACACTTGTGGCATCA A

FIG. 54 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg12-13WT (SEQ ID NO: 447) in different normal tissues.

Expression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg12-13WT (SEQ ID NO:447)in Normal and Cancerous Lung Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg12-13WT—Z25299_seg12-13WT (SEQ ID NO:447) amplicon and primersZ25299_seg12-13WTF (SEQ ID NO:448) and Z25299_seg12-13WTR (SEQ IDNO:449) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), HPRT1 (GenBankAccession No. NM 000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon (SEQID NO:380)), PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)) and GAPDH (GenBank Accession No.BC026907 (SEQ ID NO:451); GAPDH (SEQ ID NO:450) amplicon) was measuredsimilarly. For each RT sample, the expression of the above amplicon wasnormalized to the geometric mean of the quantities of the housekeepinggenes. The normalized quantity of each RT sample was then divided by themedian of the quantities of the normal post-mortem (PM) samples (samplenumbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3above), to obtain a value of fold differential expression for eachsample relative to median of the normal PM samples—these values areplotted in FIG. 55. Then the reciprocal of this ratio was calculated, toobtain a value of fold down-regulation for each sample relative tomedian of the normal PM samples—these values are plotted in FIG. 56.

FIGS. 55 and 56 are histograms showing down regulation of theabove-indicated Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous lung samples relative tothe normal samples.

As is evident from FIGS. 55 and 56, the expression of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in cancer samples, mainly in the smallcell carcinoma was lower than in the non-cancerous samples (samplenumbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3above). Notably down regulation of at least 5 fold was found in 10 outof 15 adenocarcinoma samples, 10 out of 16 squamous cell carcinomasamples, 3 out of 4 large cell carcinoma samples and in 8 out of 8 smallcells carcinoma samples.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg12-13WTF (SEQ ID NO:448) forward primer;and Z25299_seg12-13WTR (SEQ ID NO:449) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg12-13WT (SEQID NO:447).

Forward Primer (Z25299_seg12-13WTF (SEQ ID NO: 448)):AAGAAATCTGCCCAGTGCCT Reverse Primer (Z25299_seg12-13WTR (SEQ ID NO:449)): TTGATGCCACAAGTGTCAGGA Amplicon (Z25299_seg12-13WT (SEQ IDNO:447)): AAGAAATCTGCCCAGTGCCTTAGATACAAGAAACCTGAGTGCCAGAGTGACTGGCAGTGTCCAGGGAAGAAGAGATGTTGTCCTGACACTTGTGGCATCA AExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg12-13WT (SEQ ID NO:447)in Normal and Cancerous Ovary Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg12-13WT—Z25299_seg12-13WT (SEQ ID NO:447) amplicon and primersZ25299_seg12-13WTF (SEQ ID NO:448) and Z25299_seg12-13WTR (SEQ IDNO:449) was measured by real time PCR. In parallel the expression offour housekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)) and GAPDH (GenBank Accession No.BC026907 (SEQ ID NO:451); GAPDH (SEQ ID NO:450) amplicon) was measuredsimilarly. For each RT sample, the expression of the above amplicon wasnormalized to the geometric mean of the quantities of the housekeepinggenes. The normalized quantity of each RT sample was then divided by themedian of the quantities of the normal post-mortem (PM) samples (samplenumbers 45, 46, 71 and 48, Table 1 above), to obtain a value of foldup-regulation for each sample relative to median of the normal PMsamples.

FIG. 57 is a histogram showing over expression of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous Ovary samples relative tothe normal samples.

As is evident from FIG. 57, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in adenocarcinoma samples wassignificantly higher than in the non-cancerous samples (sample numbers45, 46, 71 and 48, Table 1 above). Notably an over-expression of atleast 5 fold was found in 26 out of 43 adenocarcinoma samples,specifically in 20 out of 30 serous carcinoma samples, mainly inpatients with age above 50, and in 2 out of 6 mucinous carcinomasamples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in Ovary serous carcinoma samplesversus the normal tissue samples was determined by T test as 7.72e-004.The P value for the difference in the expression levels of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in Ovary adenocarcinoma samples versusthe normal tissue samples was determined by T test as 6.46e-004.

Threshold of 5 fold over expression was found to differentiate betweenserous carcinoma and normal samples with P value of 2.16e-002 as checkedby exact Fisher test. Threshold of 5 fold over expression was found todifferentiate between adenocarcinoma and normal samples with P value of3.36e-002 as checked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg12-13WTF (SEQ ID NO:448) forward primer;and Z25299_seg12-13WTR (SEQ ID NO:449) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg12-13WT (SEQID NO:447).

Forward Primer (Z25299_seg12-13WTF (SEQ ID NO: 448)):AAGAAATCTGCCCAGTGCCT Reverse Primer (Z25299_seg12-13WTR (SEQ ID NO:449)): TTGATGCCACAAGTGTCAGGA Amplicon (Z25299_seg12-13WT (SEQ IDNO:447)): AAGAAATCTGCCCAGTGCCTTAGATACAAGAAACCTGAGTGCCAGAGTGACTGGCAGTGTCCAGGGAAGAAGAGATGTTGTCCTGACACTTGTGGCATCA A

Expression of Secretory Leukocyte Protease Inhibitor Acid-StableProteinase Inhibitor Z25299 Transcripts, which are Detectable byAmplicon as Depicted in Sequence Name Z25299 seg20 (SEQ ID NO: 452) inNormal and Cancerous Lung Tissues

Expression of Secretory leukocyte protease inhibitor Acid-stableproteinase inhibitor transcripts detectable by or according to seg20,Z25299 seg20 (SEQ ID NO: 452) amplicon and Z25299 seg20F (SEQ ID NO:453) and Z25299 seg20R (SEQ ID NO: 454) primers was measured by realtime PCR. In parallel the expression of four housekeeping genes —PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), UBC (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)) and SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (Sample Nos.47-50, 90-93, 96-99, Table 3, above)—these values are plotted in FIG.58. Then the reciprocal of this ratio was calculated, to obtain a valueof fold down-regulation for each sample relative to median of the normalPM samples—these values are plotted in FIG. 59.

FIGS. 58 and 59 are histograms showing down regulation of theabove-indicated Secretory leukocyte protease inhibitor Acid-stableproteinase inhibitor transcripts in cancerous lung samples relative tothe normal samples.

As is evident from FIGS. 58 and 59, the expression of Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitor

-   -   transcripts detectable by the above amplicon(s) in cancer        samples was significantly lower than in the non-cancerous        samples (Sample Nos. 47-50, 90-93, 96-99 Table 3). Notably down        regulation of at least 5 fold was found in 6 out of 15        adenocarcinoma samples, 9 out of 16 squamous cell carcinoma        samples, 3 out of 4 large cell carcinoma samples and in 8 out of        8 small cells carcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts detectable by the above amplicon in lung cancer samplesversus the normal tissue samples was determined by T test as 9.43E-02 inadenocarcinoma, 5.62E-02 in squamous cell carcinoma, 3.38E-01 in largecell carcinoma and 3.78E-02 in small cell carcinoma.

Threshold of 5 fold down regulation was found to differentiate betweencancer and normal samples with P value of 3.73E-02 in adenocarcinoma,1.10E-02 in squamous cell carcinoma, 2.64E-02 in large cell carcinomaand 7.14E-05 in small cell carcinomas checked by exact fisher test. Theabove values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299 seg20F (SEQ ID NO: 453) forward primer; andZ25299 seg20R (SEQ ID NO: 454) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299 seg20 (SEQ IDNO: 452).

Forward primer (SEQ ID NO: 453): CTCCTGAACCCTACTCCAAGCA Reverse primer(SEQ ID NO: 454): CAGGCGATCCTATGGAAATCC Amplicon (SEQ ID NO: 452):CTCCTGAACCCTACTCCAAGCACAGCCTCTGTCTGACTCCCTTGTCCTTCAAGAGAACTGTTCTCCAGGTCTCAGGGCCAGGATTTCCATAGGATCGCCT GExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg20 (SEQ ID NO: 452) inDifferent Normal Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg20—Z25299_seg20 (SEQ ID NO: 452) amplicon and primers Z25299_seg20F(SEQ ID NO: 453) and Z25299 seg20R (SEQ ID NO: 454) was measured by realtime PCR. In parallel the expression of four housekeeping genes—SDHA(GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the ovary samples (samplenumbers 19 and 20, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the ovary samples.

Values represent the average of duplicate experiments. Error barsindicate the minimal and maximal values obtained.

Forward Primer (Z25299_seg20F (SEQ ID NO: 453)): CTCCTGAACCCTACTCCAAGCAReverse Primer (Z25299_seg20R (SEQ ID NO: 454)): CAGGCGATCCTATGGAAATCCAmplicon (Z25299_seg20 (SEQ ID NO: 452)):CTCCTGAACCCTACTCCAAGCACAGCCTCTGTCTGACTCCCTTGTCCTTCAAGAGAACTGTTCTCCAGGTCTCAGGGCCAGGATTTCCATAGGATCGCCT G

FIG. 60 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg20 (SEQ ID NO: 452) in different normal tissues.

Expression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg23 (SEQ ID NO:455) inNormal and Cancerous Colon Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg23—Z25299_seg23 (SEQ ID NO:455) amplicon and primers Z25299_seg23F(SEQ ID NO:456) and Z25299_seg23R (SEQ ID NO:457) was measured by realtime PCR. In parallel the expression of four housekeeping genes —HPRT1(GenBank Accession No. NM_(—)000194 (SEQ ID NO: 379);amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBank Accession No.BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)),RPS27A (GenBank Accession No. NM_(—)002954 (SEQ ID NO:403); RPS27A (SEQID NO:402) amplicon) and G6PD (GenBank Accession No. NM_(—)000402 (SEQID NO:405); G6PD (SEQ ID NO:404) amplicon) was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers41, 52, 62, 63, 64, 65, 66, 67, 69, 70 and 71, Table 2 above), to obtaina value of fold up-regulation for each sample relative to median of thenormal PM samples.

FIG. 61 is a histogram showing over expression of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous Colon samples relative tothe normal samples.

As is evident from FIG. 61, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in cancer samples was higher than inthe non-cancerous samples (sample numbers 41, 52, 62, 63, 64, 65, 66,67, 69, 70 and 71, Table 2 above). Notably an over-expression of atleast 5 fold was found in 6 out of 36 adenocarcinoma samples.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg23F (SEQ ID NO:456) forward primer; andZ25299_seg23R (SEQ ID NO:457) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg23 (SEQ IDNO:455).

Forward Primer (Z25299_seg23F (SEQ ID NO:456)): CAAGCAATTGAGGGACCAGGReverse Primer (Z25299_seg23R (SEQ ID NO:457)):CAAAAAACATTGTTAATGAGAGAGATGAC Amplicon (Z25299_seg23 (SEQ ID NO:455)):CAAGCAATTGAGGGACCAGGAAGTGGATCCTCTAGAGATGAGGAGGCATTCTGCTGGATGACTTTTAAAAATGTTTTCTCCAGAGTCATCTCTCTCATTA ACAATGTTTTTTGExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg23 (SEQ ID NO:455) inNormal and Cancerous Lung Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg23—Z25299_seg23 (SEQ ID NO:455) amplicon and primers Z25299_seg23F(SEQ ID NO:456) and Z25299_seg23R (SEQ ID NO:457) was measured by realtime PCR. In parallel the expression of four housekeeping genes —HPRT1(GenBank Accession No. NM_(—)000194 (SEQ ID NO: 379);amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBank Accession No.BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)),RPS27A (GenBank Accession No. NM_(—)002954 (SEQ ID NO:403); RPS27A (SEQID NO:402) amplicon) and G6PD (GenBank Accession No. NM_(—)000402 (SEQID NO:405); G6PD (SEQ ID NO:404) amplicon) was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3 above), toobtain a value of fold differential expression for each sample relativeto median of the normal PM samples.

FIG. 62 is a histogram showing down regulation of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous lung samples relative tothe normal samples.

As is evident from FIG. 62, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in cancer samples, especially in thesmall cell carcinoma samples, was significantly lower than in thenon-cancerous samples (sample numbers 47, 48, 49, 50, 90, 91, 92, 93,96, 97, 98 and 99, Table 3 above).

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in lung cancer samples versus thenormal tissue samples was determined by T test as 1.90E-3

This value demonstrates statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg23F (SEQ ID NO:456) forward primer; andZ25299_seg23R (SEQ ID NO:457) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg23 (SEQ IDNO:455).

Forward Primer (Z25299_seg23F (SEQ ID NO:456)): CAAGCAATTGAGGGACCAGGReverse Primer (Z25299_seg23R (SEQ ID NO:457)):CAAAAAACATTGTTAATGAGAGAGATGAC Amplicon (Z25299_seg23 (SEQ ID NO:455)):CAAGCAATTGAGGGACCAGGAAGTGGATCCTCTAGAGATGAGGAGGCATTCTGCTGGATGACTTTTAAAAATGTTTTCTCCAGAGTCATCTCTCTCATTA ACAATGTTTTTTGExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg23 (SEQ ID NO:455) inDifferent Normal Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg23—Z25299_seg23 (SEQ ID NO:455) amplicon and primers Z25299_seg23F(SEQ ID NO:456) and Z25299 seg23R (SEQ ID NO:457) was measured by realtime PCR. In parallel the expression of four housekeeping genes—SDHA(GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), Ubiquitin (GenBank AccessionNo. BC000449 (SEQ ID NO:366); amplicon—Ubiquitin-amplicon (SEQ IDNO:367)), RPL19 (GenBank Accession No. NM_(—)000981 (SEQ ID NO:369);RPL19 (SEQ ID NO:368) amplicon) and TATA box (GenBank Accession No.NM_(—)003194 (SEQ ID NO:371); TATA (SEQ ID NO:370) amplicon) wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the ovary samples (samplenumbers 19 and 20, Table 5 above), to obtain a value of relativeexpression of each sample relative to median of the ovary samples.

Values represent the average of duplicate experiments. Error barsindicate the minimal and maximal values obtained.

Forward Primer (Z25299_seg23F (SEQ ID NO:456)): CAAGCAATTGAGGGACCAGGReverse Primer (Z25299_seg23R (SEQ ID NO:457)):CAAAAAACATTGTTAATGAGAGAGATGAC Amplicon (Z25299_seg23 (SEQ ID NO:455)):CAAGCAATTGAGGGACCAGGAAGTGGATCCTCTAGAGATGAGGAGGCATTCTGCTGGATGACTTTTAAAAATGTTTTCTCCAGAGTCATCTCTCTCATTA ACAATGTTTTTTG

FIG. 63 is a histogram showing expression of the Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) Z25299 transcriptswhich are detectable by amplicon as depicted in sequence nameZ25299_seg23 (SEQ ID NO: 455) in different normal samples.

Expression of Secretory Leukocyte Protease Inhibitor Acid-StableProteinase Inhibitor Z25299 Transcripts which are Detectable by Ampliconas Depicted in Sequence Name Z25299 junc13-14-21 (SEQ ID NO: 444) inNormal and Cancerous Ovary Tissues

Expression of Secretory leukocyte protease inhibitor Acid-stableproteinase transcripts detectable by or according to junc13-14-21,Z25299 junc13-14-21 (SEQ ID NO: 444) amplicon and Z25299 junc13-14-21F(SEQ ID NO: 445) and Z25299 junc13-14-21R (SEQ ID NO: 446) primers wasmeasured by real time PCR. In parallel the expression of fourhousekeeping genes —PBGD (GenBank Accession No. BC019323 (SEQ IDNO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), SDHA (GenBank Accession No. NM 004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)), and GAPDH (GenBank AccessionNo. BC026907 (SEQ ID NO:451); GAPDH (SEQ ID NO:450) amplicon wasmeasured similarly. For each RT sample, the expression of the aboveamplicon was normalized to the geometric mean of the quantities of thehousekeeping genes. The normalized quantity of each RT sample was thendivided by the median of the quantities of the normal post-mortem (PM)samples (Sample Nos. 45, 46, 48, 71 Table 1 above), to obtain a value offold up-regulation for each sample relative to median of the normal PMsamples.

FIG. 64 is a histogram showing over expression of the above-indicatedSecretory leukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts in cancerous ovary samples relative to the normal samples.The number of samples that exhibit at least 5 fold over-expression, outof the total number of samples tested is indicated in the bottom.

As is evident from FIG. 64, the expression of Secretory leukocyteprotease inhibitor Acid-stable proteinase inhibitor transcriptsdetectable by the above amplicon in cancer samples was significantlyhigher than in the non-cancerous samples (Sample Nos. 45, 46, 48, 71Table 1). Notably an over-expression of at least 5 fold was found in 14out of 30 serous adenocarcinoma, with the highest expression in samplesfrom patients with age above 50, and in 3 out of 6 mucinusadenocarcinoma samples and in 1 out of the 2 clear cell samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts detectable by the above amplicon in Ovary adenocarcinomasamples versus the non-cancerous tissue samples was determined by T testas 6.76e-03.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_junc13-14-21F (SEQ ID NO: 445) forwardprimer; and Z25299 junc13-14-21R (SEQ ID NO: 446) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_junc13-14-21(SEQ ID NO: 444).

Forward primer (SEQ ID NO: 445): ACCCCAAACCCAACTTGATTC Reverse primer(SEQ ID NO: 446): TCAGTGGTGGAGCCAAGTCTC Amplicon (SEQ ID NO: 444):ACCCCAAACCCAACTTGATTCCTGCCATATGGAGGAGGCTCTGGAGTCCTGCTCTGTGTGGTCCAGGTCCTTTCCACCCTGAGACTTGGCTCCACCACTG A

Expression of Secretory Leukocyte Protease Inhibitor Acid-StableProteinase Inhibitor Z25299 transcripts, which are Detectable byAmplicon as Depicted in Sequence Name Z25299 seg20 (SEQ ID NO: 452) inNormal and Cancerous Ovary Tissues

Expression of Secretory leukocyte protease inhibitor Acid-stableproteinase inhibitor transcripts detectable by or according to seg20,Z25299 seg20 amplicon (SEQ ID NO: 452) and Z25299 seg20F (SEQ ID NO:453) and Z25299 seg20R (SEQ ID NO: 454) primers was measured by realtime PCR. In parallel the expression of four housekeeping genes —PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), SDHA (GenBank AccessionNo. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ IDNO:365)), and GAPDH (GenBank Accession No. BC026907 (SEQ ID NO:451);GAPDH (SEQ ID NO:450) amplicon was measured similarly. For each RTsample, the expression of the above amplicon was normalized to thegeometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (Sample Nos. 45,46, 48, 71 Table 1, above), to obtain a value of fold up-regulation foreach sample relative to median of the normal PM samples.

FIG. 65 is a histogram showing over expression of the above-indicatedSecretory leukocyte protease inhibitor Acid-stable proteinasetranscripts in cancerous ovary samples relative to the normal samples.The number of samples that exhibit at least 5 fold over-expression, outof the total number of samples tested is indicated in the bottom.

As is evident from FIG. 65, the expression of Secretory leukocyteprotease inhibitor Acid-stable proteinase inhibitor transcriptsdetectable by the above amplicon in cancer samples was significantlyhigher than in the non-cancerous samples (Sample Nos. 45, 46, 48, 71Table 1). Notably an over-expression of at least 5 fold was found in 21out of 30 serous adenocarcinoma, with the highest expression in samplesfrom patients with age above 50, and in 4 out of 6 mucinusadenocarcinoma samples and in 2 out of the 2 clear cell samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts detectable by the above amplicon in Ovary adenocarcinomasamples versus the non-cancerous (benign and normal) tissue samples wasdetermined by T test as 4.97e-04.

Threshold of 5 fold over expression was found to differentiate betweenadenocarcinoma and non-cancerous samples (benign and normal) with Pvalue of 1.32e-03 as checked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299 seg20F (SEQ ID NO: 453) forward primer; andZ25299 seg20R (SEQ ID NO: 454) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299 seg20 (SEQ IDNO: 452).

Forward primer (SEQ ID NO: 453): CTCCTGAACCCTACTCCAAGCA Reverse primer(SEQ ID NO: 454): CAGGCGATCCTATGGAAATCC Amplicon (SEQ ID NO: 452):CTCCTGAACCCTACTCCAAGCACAGCCTCTGTCTGACTCCCTTGTCCTTCAAGAGAACTGTTCTCCAGGTCTCAGGGCCAGGATTTCCATAGGATCGCCT G

Expression of Secretory Leukocyte Protease Inhibitor Acid-StableProteinase Inhibitor Z25299 Transcripts, which are Detectable byAmplicon as Depicted in Sequence Name Z25299 seg23 (SEQ ID NO: 455) inNormal and Cancerous Ovary Tissues

Expression of Secretory leukocyte protease inhibitor Acid-stableproteinase inhibitor transcripts detectable by or according to seg23,Z25299 seg23 (SEQ ID NO: 455) amplicon and Z25299 seg23F (SEQ ID NO:456) and Z25299 seg23R (SEQ ID NO: 457) primers was measured by realtime PCR. In parallel the expression of four housekeeping genes —PBGD(GenBank Accession No. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon(SEQ ID NO:382)), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), SDHA (GenBank AccessionNo. NM_(—)004168 (SEQ ID NO:364); amplicon—SDHA-amplicon (SEQ IDNO:365)), and GAPDH (GenBank Accession No. BC026907 (SEQ ID NO:451);GAPDH (SEQ ID NO:450) amplicon was measured similarly. For each RTsample, the expression of the above amplicon was normalized to thegeometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (Sample Nos. 45,46, 48, 71 Table 1, above), to obtain a value of fold up-regulation foreach sample relative to median of the normal PM samples.

FIG. 66 is a histogram showing over expression of the above-indicatedSecretory leukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts in cancerous ovary samples relative to the normal samples.The number of samples that exhibit at least 5 fold over-expression, outof the total number of samples tested is indicated in the bottom.

As is evident from FIG. 66, the expression of Secretory leukocyteprotease inhibitor Acid-stable proteinase inhibitor transcriptsdetectable by the above amplicon in cancer samples was significantlyhigher than in the non-cancerous samples (Sample Nos. 45, 46, 48, 71Table 1). Notably an over-expression of at least 5 fold was found in 21out of 30 serous adenocarcinoma, with the highest expression in samplesfrom patients with age above 50, and in 3 out of 6 mucinusadenocarcinoma samples and in 2 out of the 2 clear cell samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Secretoryleukocyte protease inhibitor Acid-stable proteinase inhibitortranscripts detectable by the above amplicon in Ovary adenocarcinomasamples versus the non-cancerous tissue samples was determined by T testas 1.42e-04.

Threshold of 5 fold over expression was found to differentiate betweenadenocarcinoma and non-cancerous samples with P value of 3.10e-03 aschecked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299 seg23F (SEQ ID NO: 456) forward primer; andZ25299 seg23R (SEQ ID NO: 457) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299 seg23 (SEQ IDNO: 455).

Forward primer (SEQ ID NO: 456): CAAGCAATTGAGGGACCAGG Reverse primer(SEQ ID NO: 457): CAAAAAACATTGTTAATGAGAGAGATGAC Amplicon (Seq id no:455): CAAGCAATTGAGGGACCAGGAAGTGGATCCTCTAGAGATGAGGAGGCATTCTGCTGGATGACTTTTAAAAATGTTTTCTCCAGAGTCATCTCTCTCATTA ACAATGTTTTTTGExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_junc13-14-21 (SEQ ID NO:444) in Normal and Cancerous Lung Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according tojunc13-14-21—Z25299_junc13-14-21 (SEQ ID NO: 444) amplicon and primersZ25299_junc13-14-21-F (SEQ ID NO: 445) and junc13-14-21-R (SEQ ID NO:446) was measured by real time PCR. In parallel the expression of fourhousekeeping genes—SDHA (GenBank Accession No. NM_(—)004168 (SEQ IDNO:364); amplicon—SDHA-amplicon (SEQ ID NO:365)), HPRT1 (GenBankAccession No. NM_(—)000194 (SEQ ID NO: 379); amplicon—HPRT1-amplicon(SEQ ID NO:380)), PBGD (GenBank Accession No. BC019323 (SEQ ID NO:381);amplicon—PBGD-amplicon (SEQ ID NO:382)) and GAPDH (GenBank Accession No.BC026907 (SEQ ID NO:451); GAPDH (SEQ ID NO:450) amplicon) was measuredsimilarly. For each RT sample, the expression of the above amplicon wasnormalized to the geometric mean of the quantities of the housekeepinggenes. The normalized quantity of each RT sample was then divided by themedian of the quantities of the normal post-mortem (PM) samples (samplenumbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3above), to obtain a value of fold differential expression for eachsample relative to median of the normal PM samples—these values areplotted in FIG. 67.

FIG. 67 is a histogram showing down regulation of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous lung samples relative tothe normal samples.

As is evident from FIG. 67, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in cancer samples, mainly in the smallcell carcinoma was lower than in the non-cancerous samples (samplenumbers 47, 48, 49, 50, 90, 91, 92, 93, 96, 97, 98 and 99, Table 3above).

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in lung cancerous samples versus thenormal tissue samples was determined by T test as 1.98e-04. This valuedemonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_junc13-14-21F (SEQ ID NO: 445) forwardprimer; and Z25299_junc13-14-21R (SEQ ID NO: 446) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_junc13-14-21(SEQ ID NO: 444).

Forward Primer (Z25299_junc13-14-21F (SEQ ID NO: 445)):ACCCCAAACCCAACTTGATTC Reverse Primer (Z25299_junc13-14-21R (SEQ ID NO:446)): TCAGTGGTGGAGCCAAGTCTC Amplicon (Z25299_seg13-14-21 (SEQ ID NO:444): ACCCCAAACCCAACTTGATTCCTGCCATATGGAGGAGGCTCTGGAGTCCTGCTCTGTGTGGTCCAGGTCCTTTCCACCCTGAGACTTGGCTCCACCACTG AExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg20 (SEQ ID NO: 452) inNormal and Cancerous Colon Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg20—Z25299_seg20 (SEQ ID NO: 452) amplicon and primers Z25299_seg20F(SEQ ID NO: 453) and Z25299_seg20R (SEQ ID NO: 454) was measured by realtime PCR. In parallel the expression of four housekeeping genes —HPRT1(GenBank Accession No. NM_(—)000194 (SEQ ID NO: 379);amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBank Accession No.BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ ID NO:382)),RPS27A (GenBank Accession No. NM_(—)002954 (SEQ ID NO:403); RPS27A (SEQID NO:402) amplicon) and G6PD (GenBank Accession No. NM_(—)000402 (SEQID NO:405); G6PD (SEQ ID NO:404) amplicon) was measured similarly. Foreach RT sample, the expression of the above amplicon was normalized tothe geometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers41, 52, 62, 63, 64, 65, 66, 67, 69, 70 and 71, Table 2 above), to obtaina value of fold up-regulation for each sample relative to median of thenormal PM samples.

FIG. 68 is a histogram showing over expression of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous Colon samples relative tothe normal samples.

As is evident from FIG. 68, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon was higher in several cancer samplesthan in the non-cancerous samples (sample numbers 41, 52, 62, 63, 64,65, 66, 67, 69, 70 and 71, Table 2 above). Notably an over-expression ofat least 5 fold was found in 7 out of 36 adenocarcinoma samples.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg20F (SEQ ID NO: 453) forward primer; andZ25299_seg20R (SEQ ID NO: 454) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg20 (SEQ IDNO: 452).

Forward Primer (Z25299_seg20F (SEQ ID NO: 453)): CTCCTGAACCCTACTCCAAGCAReverse Primer (Z25299_seg20R (SEQ ID NO: 454)): CAGGCGATCCTATGGAAATCCAmplicon (Z25299_seg20 (SEQ ID NO: 452)):CTCCTGAACCCTACTCCAAGCACAGCCTCTGTCTGACTCCCTTGTCCTTCAAGAGAACTGTTCTCCAGGTCTCAGGGCCAGGATTTCCATAGGATCGCCT GExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg20 (SEQ ID NO: 452) inNormal and Cancerous Breast Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg20—Z25299_seg20 (SEQ ID NO: 452) amplicon and primers Z25299_seg20F(SEQ ID NO: 453) and Z25299_seg20R (SEQ ID NO: 454) was measured by realtime PCR. In parallel the expression of four housekeeping genes—G6PD(GenBank Accession No. NM_(—)000402 (SEQ ID NO:405); G6PD (SEQ IDNO:404) amplicon), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBank AccessionNo. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ ID NO:382))and SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)) was measured similarly. For eachRT sample, the expression of the above amplicon was normalized to thegeometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers57, 59, 60, 63, 66, 64, 56, 65, 67 and 58, Table 4 above), to obtain avalue of expression for each sample relative to median of the normal PMsamples. Then the reciprocal of this ratio was calculated, to obtain avalue of fold down-regulation for each sample relative to median of thenormal PM samples

FIG. 69 is a histogram showing down regulation of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous breast samples relativeto the normal samples.

As is evident from FIG. 69, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon was lower in the cancer samples than inthe in the non-cancerous samples (sample numbers 57, 59, 60, 63, 66, 64,56, 65, 67 and 58, Table 4 above). Notably down regulation of at least 5fold was found in 11 out of 28 adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

The P value for the difference in the expression levels of Homo sapienssecretory leukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon in breast adenocarcinoma samples versusthe normal tissue samples was determined by T test as 3.42e-03.

Threshold of 5 fold over expression was found to differentiate betweenadenocarcinoma and normal samples with P value of 2.16e-002 as checkedby exact Fisher test. Threshold of 5 fold over expression was found todifferentiate between adenocarcinoma and normal samples with P value of1.52e-02 as checked by exact Fisher test.

The above values demonstrate statistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg20F (SEQ ID NO: 453) forward primer; andZ25299_seg20R (SEQ ID NO: 454) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg20 (SEQ IDNO: 452).

Forward Primer (Z25299_seg20F (SEQ ID NO: 453)): CTCCTGAACCCTACTCCAAGCAReverse Primer (Z25299_seg20R (SEQ ID NO: 454)): CAGGCGATCCTATGGAAATCCAmplicon (Z25299_seg20 (SEQ ID NO: 452)):CTCCTGAACCCTACTCCAAGCACAGCCTCTGTCTGACTCCCTTGTCCTTCAAGAGAACTGTTCTCCAGGTCTCAGGGCCAGGATTTCCATAGGATCGCCT GExpression of Homo sapiens Secretory Leukocyte Protease Inhibitor(Antileukoproteinase) Z25299 Transcripts which are Detectable byAmplicon as Depicted in Sequence Name Z25299_seg23 (SEQ ID NO:455) inNormal and Cancerous Breast Tissues

Expression of Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable by or according toseg23—Z25299_seg23 (SEQ ID NO:455) amplicon and primers Z25299_seg23F(SEQ ID NO:456) and Z25299_seg23R (SEQ ID NO:457) was measured by realtime PCR. In parallel the expression of four housekeeping genes—G6PD(GenBank Accession No. NM_(—)000402 (SEQ ID NO:405); G6PD (SEQ IDNO:404) amplicon), HPRT1 (GenBank Accession No. NM_(—)000194 (SEQ ID NO:379); amplicon—HPRT1-amplicon (SEQ ID NO:380)), PBGD (GenBank AccessionNo. BC019323 (SEQ ID NO:381); amplicon—PBGD-amplicon (SEQ ID NO:382))and SDHA (GenBank Accession No. NM_(—)004168 (SEQ ID NO:364);amplicon—SDHA-amplicon (SEQ ID NO:365)) was measured similarly. For eachRT sample, the expression of the above amplicon was normalized to thegeometric mean of the quantities of the housekeeping genes. Thenormalized quantity of each RT sample was then divided by the median ofthe quantities of the normal post-mortem (PM) samples (sample numbers57, 59, 60, 63, 66, 64, 56, 65, 67 and 58, Table 4 above), to obtain avalue of expression for each sample relative to median of the normal PMsamples. Then the reciprocal of this ratio was calculated, to obtain avalue of fold down-regulation for each sample relative to median of thenormal PM samples

FIG. 70 is a histogram showing down regulation of the above-indicatedHomo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts in cancerous breast samples relativeto the normal samples.

As is evident from FIG. 70, the expression of Homo sapiens secretoryleukocyte protease inhibitor (antileukoproteinase) transcriptsdetectable by the above amplicon was lower in the cancer samples than inthe in the non-cancerous samples (sample numbers 57, 59, 60, 63, 66, 64,56, 65, 67 and 58, Table 4 above). Notably down regulation of at least 5fold was found in 12 out of 28 adenocarcinoma samples.

Statistical analysis was applied to verify the significance of theseresults, as described below.

Threshold of 5 fold over expression was found to differentiate betweenadenocarcinoma and normal samples with P value of 2.16e-002 as checkedby exact Fisher test. Threshold of 5 fold over expression was found todifferentiate between adenocarcinoma and normal samples with P value of1.12e-02 as checked by exact Fisher test. This value demonstratesstatistical significance of the results.

Primer pairs are also optionally and preferably encompassed within thepresent invention; for example, for the above experiment, the followingprimer pair was used as a non-limiting illustrative example only of asuitable primer pair: Z25299_seg23F (SEQ ID NO:456) forward primer; andZ25299_seg23R (SEQ ID NO:457) reverse primer.

The present invention also preferably encompasses any amplicon obtainedthrough the use of any suitable primer pair; for example, for the aboveexperiment, the following amplicon was obtained as a non-limitingillustrative example only of a suitable amplicon: Z25299_seg23 (SEQ IDNO:455).

Forward Primer (Z25299_seg23F (SEQ ID NO:456)): CAAGCAATTGAGGGACCAGGReverse Primer (Z25299_seg23R (SEQ ID NO:457)):CAAAAAACATTGTTAATGAGAGAGATGAC Amplicon (Z25299_seg23 (SEQ ID NO:455)):CAAGCAATTGAGGGACCAGGAAGTGGATCCTCTAGAGATGAGGAGGCATTCTGCTGGATGACTTTTAAAAATGTTTTCTCCAGAGTCATCTCTCTCATTA ACAATGTTTTTTG

Homo sapiens secretory leukocyte protease inhibitor(antileukoproteinase) transcripts detectable byamplicon—Z25299_junc13-14-21 (SEQ ID NO: 444) amplicon and primersZ25299_junc13-14-21-F (SEQ ID NO: 445) and Z25299_junc13-14-21-R (SEQ IDNO: 446) did not show any differential expression in one experimentcarried out with each of the following cancer panels: colon cancer andbreast cancer.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims. All publications, patents and patentapplications mentioned in this specification are herein incorporated intheir entirety by reference into the specification, to the same extentas if each individual publication, patent or patent application wasspecifically and individually indicated to be incorporated herein byreference. In addition, citation or identification of any reference inthis application shall not be construed as an admission that suchreference is available as prior art to the present invention.

1-134. (canceled)
 135. An isolated polynucleotide comprising thepolynucleotide sequence set forth in a member selected from the groupconsisting of SEQ ID NOs: 1-15, 61-64, 96-98, 114-126, 189-193, 211-214,235, 244, 252-253, 305-306, 340-344, 458, 32-60, 71-95, 103-113,139-188, 196-210, 220-234, 237-243, 246-251, 256-304, 309-339, 350-358,502-530, 363, 414, 417, 420, 424, 427, 431, 434, 437, 444, 447, 452 and455, or a sequence at least about 95% identical thereto.
 136. Anisolated polypeptide comprising the polypeptide sequence set forth in amember selected from the group consisting of SEQ ID NOs: 16-31, 65-70,99-102, 127-138, 194-195, 215-219, 236, 245, 254-255, 307-308, 345-349,459-501, 576-591 and 592, or a sequence at least about 95% identicalthereto.
 137. An expression vector comprising the polynucleotidesequence according to claim
 135. 138. A host cell comprising the vectorof claim
 137. 139. A process for producing a polypeptide comprising:culturing the host cell according to claim 138 under conditions suitableto produce the polypeptide encoded by said polynucleotide; andrecovering said polypeptide.
 140. An isolated primer pair for amplifyingthe polynucleotide sequence of claim 135, comprising the pair of nucleicacid sequences selected from the group consisting of: SEQ NOs: 361-362,415-416, 418-419, 421-422, 425-426, 428-429, 432-433, 435-436, 438-439,445-446, 448-449, 453-454 and 456-457.
 141. An antibody to specificallybind to the polypeptide of claim
 136. 142. A kit for detecting a diseaseselected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammatory disease and cancer, thekit comprising at least one primer pair of claim 140 for detecting thepolynucleotide sequence set forth in a member selected from the groupconsisting of SEQ ID NOs:, 1-15, 61-64, 96-98, 114-126, 189-193,211-214, 235, 244, 252-253, 305-306, 340-344, 458, 32-60, 71-95,103-113, 139-188, 196-210, 220-234, 237-243, 246-251, 256-304, 309-339,350-358, 502-530, 363, 414, 417, 420, 424, 427, 431, 434, 437, 444, 447,452 and
 455. 143. A kit for detecting a disease selected from the groupconsisting of cardiovascular disease, cerebrovascular disease, chronicinflammatory disease and cancer, the kit comprising the antibody ofclaim 141 for detecting the polypeptide sequence set forth in a memberselected from the group consisting of SEQ ID NOs:, 16-31, 65-70, 99-102,127-138, 194-195, 215-219, 236, 245, 254-255, 307-308, 345-349, 459-501,576-591 and
 592. 144. The kit of claim 143, wherein said kit furthercomprises at least one immunoassay reagent.
 145. The kit of claim 144,wherein said immunoassay is selected from the group consisting of anenzyme linked immunosorbent assay (ELISA), an immunoprecipitation assay,an immunofluorescence analysis, an enzyme immunoassay (EIA), aradioimmunoassay (RIA), or a Western blot analysis.
 146. A method fordetecting a disease selected from the group consisting of cardiovasculardisease, cerebrovascular disease, chronic inflammatory disease andcancer, the method comprising detecting overexpression of thepolynucleotide sequence set forth in a member selected from the groupconsisting of SEQ ID NOs: 1-15, 61-64, 96-98, 114-126, 189-193, 211-214,235, 244, 252-253, 305-306, 340-344, 458, 32-60, 71-95, 103-113,139-188, 196-210, 220-234, 237-243, 246-251, 256-304, 309-339, 350-358,502-530, 363, 414, 417, 420, 424, 427, 431, 434, 437, 444, 447, 452,455, or a sequence at least about 95% identical thereto in a sample froma patient.
 147. The method of claim 146, wherein said detectingoverexpression comprises performing nucleic acid amplification.
 148. Themethod of claim 146, wherein the disease is cardiovascular disease, andis selected from the group consisting of myocardial infarct, acutecoronary syndrome, coronary artery disease, angina pectoris (stable andunstable), cardiomyopathy, myocarditis, congestive heart failure or anytype of heart failure, reinfarction, assessment of thrombolytic therapy,assessment of myocardial infarct size, differential diagnosis betweenheart-related versus lung-related conditions (such as pulmonaryembolism), the differential diagnosis of Dyspnea, cardiac valves relatedconditions, vascular disease, cardiac death, from arrhythmia or anyother heart related reason; rejection of a transplanted heart;conditions that lead to heart failure including myocardial infarction,angina, arrhythmias, valvular diseases, atrial and/or ventricular septaldefects; conditions that cause atrial and or ventricular wall volumeoverload, including systemic arterial hypertension, pulmonaryhypertension and pulmonary embolism; conditions which have similarclinical symptoms as heart failure and as states that cause atrial andor ventricular pressure-overload, where the differential diagnosisbetween these conditions to the latter is of clinical importanceincluding breathing difficulty and/or hypoxia due to pulmonary disease,anemia or anxiety.
 149. The method of claim 146, wherein the disease iscerebrovascular disease, and is selected from the group consisting ofany type of stroke or neural tissue injury, or any type ofcerebrovascular accident, ischemic stroke, hemorrhagic stroke ortransient ischemic attacks, thrombotic, embolic, lacunar orhypoperfusion types of strokes, brain trauma.
 150. The method of claim146, wherein the disease is chronic inflammatory disease, and isselected from the group consisting of diseases where an inflammatoryprocess plays a substantial role, such as hypercholesterolemia,diabetes, atherosclerosis, inflammation that involves bloodvessels—whether acute or chronic including the coronary arteries andblood vessels of the brain, myocardial infarction, cerebral stroke,peripheral vascular disease, vasculitis, polyarteritis nodosa, ANCAassociated small vessel vasculitis, Churg-Strauss syndrome,Henoch-Schonlein purpura, scleroderma, thromboangiitis obliterans,temporal arteritis, Takayasu's arteritis, hypersensitivity vasculitis,Kawasaki disease, Behçet syndrome, and their complications includingcoronary disease, angina pectoris, deep vein thrombosis, renal disease,diabetic nephropathy, lupus nephritis, renal artery thrombosis, renalartery stenosis, atheroembolic disease of the renal arteries, renal veinthrombosis, hemolytic uremic syndrome, thrombotic thrombocytopenicpurpura, arteriolar nephrosclerosis, preeclampsia, eclampsia,albuminuria, microalbuminuria, glomerulonephritis, renal failure,hypertension, uremia, cerebrovascular disease, peripheral vasculardisease, intermittent claudication, abdominal angina;rheumatic/autoimmune diseases that involve systemic immune reactionincluding rheumatoid arthritis, scleroderma, mixed connective tissuedisease, Sjogren syndrome, ankylosing spondylitis, spondyloarthropathy,psoriasis, psoriatic arthritis, myositis and systemic lupuserythematosus; acute and/or chronic infective processes that involvesystemic immune reaction including pneumonia, bacteremia, sepsis,pyelonephritis, cellulitis, osteomyelitis, meningitis and viralhepatitis; malignant and idiopathic processes that involve systemicimmune reaction and/or proliferation of immune cells includinggranulomatous disorders, Wegener's granulomatosis, lymphomatoidgranulomatosis/polymorphic reticulosis, idiopathic midline granuloma,multiple myeloma, Waldenstrom's macroglobulinemia, Castleman's disease,amyloidosis, lymphoma, histiocytosis, renal cell carcinoma andparaneoplastic syndromes; conditions where CRP was shown to have apositive correlation with the presence of the condition including weightloss, anorexia-cachexia syndrome, extent of disease, recurrence inadvanced cancer, diabetes (types 1 & 2), obesity, hypertension, pretermdelivery; conditions which have similar symptoms, signs andcomplications as the conditions above and where the differentialdiagnosis between them and the conditions above is of clinicalimportance including other (non vascular) causes of heart disease, renaldisease and cerebral disease; other (non rheumatic) causes ofarthropathy and musculoskeletal pain; other causes of non-specificsymptoms and signs such as fever of unknown origin, loss of appetite,weight loss, nonspecific pains, breathing difficulties, anxiety, or anycombination thereof, or any disease disorder or condition associatedwith inflammation.
 151. The method of claim 146, wherein the disease iscancer, and is selected from the group consisting of colon cancer,breast cancer, ovarian cancer, prostate cancer, lung cancer, and whereinthe cancer is invasive or metastatic.
 152. A method for detecting adisease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, themethod comprising detecting the polypeptide sequence set forth in amember selected from the group consisting of SEQ ID NOs:, 16-31, 65-70,99-102, 127-138, 194-195, 215-219, 236, 245, 254-255, 307-308, 345-349,459-501, 576-592 in a sample from a patient.
 153. The method of claim152, wherein said detecting comprises detecting binding of the antibodyof claim 7 to the polypeptide in said sample from said patient.
 154. Themethod of claim 153, wherein the disease is cardiovascular disease, andis selected from the group consisting of myocardial infarct, acutecoronary syndrome, coronary artery disease, angina pectoris (stable andunstable), cardiomyopathy, myocarditis, congestive heart failure or anytype of heart failure, reinfarction, assessment of thrombolytic therapy,assessment of myocardial infarct size, differential diagnosis betweenheart-related versus lung-related conditions (such as pulmonaryembolism), the differential diagnosis of Dyspnea, cardiac valves relatedconditions, vascular disease, cardiac death, from arrhythmia or anyother heart related reason; rejection of a transplanted heart;conditions that lead to heart failure including myocardial infarction,angina, arrhythmias, valvular diseases, atrial and/or ventricular septaldefects; conditions that cause atrial and or ventricular wall volumeoverload, including systemic arterial hypertension, pulmonaryhypertension and pulmonary embolism; conditions which have similarclinical symptoms as heart failure and as states that cause atrial andor ventricular pressure-overload, where the differential diagnosisbetween these conditions to the latter is of clinical importanceincluding breathing difficulty and/or hypoxia due to pulmonary disease,anemia or anxiety.
 155. The method of claim 153, wherein the disease iscerebrovascular disease, and is selected from the group consisting ofany type of stroke or neural tissue injury, or any type ofcerebrovascular accident, ischemic stroke, hemorrhagic stroke ortransient ischemic attacks, thrombotic, embolic, lacunar orhypoperfusion types of strokes, brain trauma.
 156. The method of claim153, wherein the disease is chronic inflammation disease, and isselected from the group consisting of diseases where an inflammatoryprocess plays a substantial role, such as hypercholesterolemia,diabetes, atherosclerosis, inflammation that involves bloodvessels—whether acute or chronic including the coronary arteries andblood vessels of the brain, myocardial infarction, cerebral stroke,peripheral vascular disease, vasculitis, polyarteritis nodosa, ANCAassociated small vessel vasculitis, Churg-Strauss syndrome,Henoch-Schonlein purpura, scleroderma, thromboangiitis obliterans,temporal arteritis, Takayasu's arteritis, hypersensitivity vasculitis,Kawasaki disease, Behçet syndrome, and their complications includingcoronary disease, angina pectoris, deep vein thrombosis, renal disease,diabetic nephropathy, lupus nephritis, renal artery thrombosis, renalartery stenosis, atheroembolic disease of the renal arteries, renal veinthrombosis, hemolytic uremic syndrome, thrombotic thrombocytopenicpurpura, arteriolar nephrosclerosis, preeclampsia, eclampsia,albuminuria, microalbuminuria, glomerulonephritis, renal failure,hypertension, uremia, cerebrovascular disease, peripheral vasculardisease, intermittent claudication, abdominal angina;rheumatic/autoimmune diseases that involve systemic immune reactionincluding rheumatoid arthritis, scleroderma, mixed connective tissuedisease, Sjogren syndrome, ankylosing spondylitis, spondyloarthropathy,psoriasis, psoriatic arthritis, myositis and systemic lupuserythematosus; acute and/or chronic infective processes that involvesystemic immune reaction including pneumonia, bacteremia, sepsis,pyelonephritis, cellulitis, osteomyelitis, meningitis and viralhepatitis; malignant and idiopathic processes that involve systemicimmune reaction and/or proliferation of immune cells includinggranulomatous disorders, Wegener's granulomatosis, lymphomatoidgranulomatosis/polymorphic reticulosis, idiopathic midline granuloma,multiple myeloma, Waldenstrom's macroglobulinemia, Castleman's disease,amyloidosis, lymphoma, histiocytosis, renal cell carcinoma andparaneoplastic syndromes; conditions where CRP was shown to have apositive correlation with the presence of the condition including weightloss, anorexia-cachexia syndrome, extent of disease, recurrence inadvanced cancer, diabetes (types 1 & 2), obesity, hypertension, pretermdelivery; conditions which have similar symptoms, signs andcomplications as the conditions above and where the differentialdiagnosis between them and the conditions above is of clinicalimportance including other (non vascular) causes of heart disease, renaldisease and cerebral disease; other (non rheumatic) causes ofarthropathy and musculoskeletal pain; other causes of non-specificsymptoms and signs such as fever of unknown origin, loss of appetite,weight loss, nonspecific pains, breathing difficulties, anxiety, or anycombination thereof, or any disease disorder or condition associatedwith inflammation.
 157. The method of claim 153, wherein the disease iscancer, and is selected from the group consisting of colon cancer,breast cancer, ovarian cancer, prostate cancer, lung cancer, and whereinthe cancer is invasive or metastatic.
 158. A biomarker for detecting adisease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, thebiomarker, comprising said polypeptide of claim 136, marked with alabel.
 159. A method to screen for or to diagnose a disease selectedfrom the group consisting of cardiovascular disease, cerebrovasculardisease, chronic inflammation disease and cancer, the method comprisingdetecting the disease with the biomarker of claim
 158. 160. A method formonitoring disease progression, treatment efficacy or relapse of adisease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, themethod comprising detecting the disease with the biomarker of claim 158.161. A method of selecting a therapy for a disease selected from thegroup consisting of cardiovascular disease, cerebrovascular disease,chronic inflammation disease and cancer, the method, comprisingdetecting the disease with the biomarker of claim 158 and selecting atherapy according to said detection.
 162. A biomarker for detecting adisease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, thebiomarker, comprising the nucleotide acid sequence set forth in themember selected from the group consisting of SEQ ID NOs: 1-15, 61-64,96-98, 114-126, 189-193, 211-214, 235, 244, 252-253, 305-306, 340-344,458, 32-60, 71-95, 103-113, 139-188, 196-210, 220-234, 237-243, 246-251,256-304, 309-339, 350-358, 502-530, 363, 414, 417, 420, 424, 427, 431,434, 437, 444, 447, 452, 455, or a sequence at least about 95% identicalthereto, marked with a label.
 163. A method to screen for or to diagnosea disease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, themethod comprising detecting the disease with the biomarker of claim 162.164. A method for monitoring disease progression, treatment efficacy orrelapse of a disease selected from the group consisting ofcardiovascular disease, cerebrovascular disease, chronic inflammationdisease and cancer, the method comprising detecting the disease with thebiomarker of claim
 162. 165. A method of selecting a therapy for adisease selected from the group consisting of cardiovascular disease,cerebrovascular disease, chronic inflammation disease and cancer, themethod comprising detecting the disease with the biomarker of claim 162and selecting a therapy according to said detection.